Data modification

Let’s start by loading all the necessary libraries.

Now now let’s load the Breast Cancer Proteomes data: https://www.kaggle.com/piotrgrabo/breastcancerproteomes

###loading the data
clinical <- read.csv("BC_data/clinical_data_breast_cancer.csv") 
genes <- read.csv("BC_data/PAM50_proteins.csv")
proteomes <- read.csv("BC_data/77_cancer_proteomes_CPTAC_itraq.csv")

The patient IDs are in a different format in the clinical dataset and the proteomic data set. This bit of code reformats the id in the clinical data set to allow joining of the two data sets on this variable.

###proteomes data modification
n <- proteomes$RefSeq_accession_number
proteomes <- as.data.frame(t(proteomes[,4:86]))
colnames(proteomes) <- n #add refseq
proteomes <- cbind(rownames(proteomes), data.frame(proteomes, row.names=NULL)) #separate the sample ID
colnames(proteomes)[1] <- "Complete.TCGA.ID" #the same name of column in clinical data

###sample ID
get_sample_id <- function(proteome_id) {
  x = substr(proteome_id, 4, 7)
  y = substr(proteome_id, 0, 2)
  paste("TCGA",y,x,sep="-")
}
proteomes$Complete.TCGA.ID <- sapply(proteomes$Complete.TCGA.ID, get_sample_id)
proteomes_id <- proteomes

Now let’s count the missing data by column and plots a graph to show the proportion of missing data for each variable.

###missing data
NA_counts <- colSums(is.na(proteomes))/nrow(proteomes)
plot(sort(NA_counts, decreasing = TRUE), col = 'blue', type = 'h', xlab = "index of proteome", 
     ylab="proportion of missing data", main = "Missing data for proteome data")

length(NA_counts[NA_counts>0.25]) #2251 missing data
## [1] 2251
#remove variables with >25% missing data
proteomes <- proteomes[ , colSums(is.na(proteomes))  / nrow(proteomes) < 0.25]
for (i in which(sapply(proteomes, is.numeric))) { #loop to impute means for remaining missing data
  proteomes[is.na(proteomes[, i]), i] <- mean(proteomes[, i],  na.rm = TRUE)
}
data <-  inner_join(clinical, proteomes, by = "Complete.TCGA.ID") #inner join to create full data
colnames(data)[3] <- "diag_age" #col name change for 3 column

How many patients there are with a given molecular subtypes of breast cancer?

###barplot
(ggplot(data, aes(x=PAM50.mRNA, fill=PAM50.mRNA)) + geom_bar() + ggtitle("Breast Cancer Subtype")) 

PCA and T-SNE Analysis

###PCA
data.pca <- prcomp(data[,32:length(data)], center = TRUE, scale. = TRUE)
summary(data.pca)
## Importance of components:
##                            PC1      PC2      PC3      PC4      PC5      PC6
## Standard deviation     33.3456 28.50017 26.60960 21.11253 19.30501 17.69423
## Proportion of Variance  0.1079  0.07885  0.06874  0.04327  0.03618  0.03039
## Cumulative Proportion   0.1079  0.18680  0.25553  0.29881  0.33499  0.36538
##                            PC7      PC8      PC9     PC10     PC11     PC12
## Standard deviation     16.3953 15.42007 15.20367 14.64010 14.37497 13.29314
## Proportion of Variance  0.0261  0.02308  0.02244  0.02081  0.02006  0.01715
## Cumulative Proportion   0.3915  0.41456  0.43700  0.45780  0.47786  0.49502
##                            PC13     PC14     PC15     PC16     PC17     PC18
## Standard deviation     12.97493 12.89127 12.43970 11.99729 11.84122 11.51675
## Proportion of Variance  0.01634  0.01613  0.01502  0.01397  0.01361  0.01288
## Cumulative Proportion   0.51136  0.52749  0.54252  0.55649  0.57010  0.58298
##                            PC19    PC20     PC21     PC22     PC23     PC24
## Standard deviation     11.38225 11.2543 11.09442 10.92804 10.84507 10.59910
## Proportion of Variance  0.01258  0.0123  0.01195  0.01159  0.01142  0.01091
## Cumulative Proportion   0.59555  0.6079  0.61980  0.63139  0.64281  0.65372
##                           PC25     PC26     PC27    PC28    PC29    PC30
## Standard deviation     10.4020 10.27133 10.03670 9.87831 9.82485 9.79822
## Proportion of Variance  0.0105  0.01024  0.00978 0.00947 0.00937 0.00932
## Cumulative Proportion   0.6642  0.67446  0.68424 0.69371 0.70308 0.71240
##                           PC31   PC32   PC33    PC34    PC35    PC36    PC37
## Standard deviation     9.69887 9.6311 9.4116 9.38675 9.29474 9.22082 9.05199
## Proportion of Variance 0.00913 0.0090 0.0086 0.00855 0.00839 0.00825 0.00795
## Cumulative Proportion  0.72154 0.7305 0.7391 0.74769 0.75608 0.76433 0.77229
##                           PC38    PC39    PC40    PC41    PC42   PC43    PC44
## Standard deviation     8.95921 8.92831 8.87769 8.79547 8.67509 8.6108 8.55630
## Proportion of Variance 0.00779 0.00774 0.00765 0.00751 0.00731 0.0072 0.00711
## Cumulative Proportion  0.78008 0.78782 0.79547 0.80298 0.81029 0.8175 0.82459
##                           PC45    PC46    PC47    PC48    PC49    PC50    PC51
## Standard deviation     8.47389 8.38387 8.27060 8.20864 8.14506 8.07420 8.02796
## Proportion of Variance 0.00697 0.00682 0.00664 0.00654 0.00644 0.00633 0.00626
## Cumulative Proportion  0.83156 0.83839 0.84503 0.85157 0.85801 0.86434 0.87059
##                           PC52    PC53    PC54    PC55    PC56   PC57    PC58
## Standard deviation     7.94363 7.89784 7.88287 7.80878 7.77427 7.6621 7.61888
## Proportion of Variance 0.00613 0.00606 0.00603 0.00592 0.00587 0.0057 0.00564
## Cumulative Proportion  0.87672 0.88277 0.88881 0.89473 0.90059 0.9063 0.91193
##                           PC59   PC60    PC61    PC62    PC63    PC64    PC65
## Standard deviation     7.54252 7.4585 7.35522 7.26737 7.21361 7.17180 7.12951
## Proportion of Variance 0.00552 0.0054 0.00525 0.00513 0.00505 0.00499 0.00493
## Cumulative Proportion  0.91745 0.9228 0.92810 0.93323 0.93828 0.94327 0.94821
##                           PC66    PC67    PC68    PC69    PC70    PC71    PC72
## Standard deviation     7.01827 6.93988 6.88758 6.74930 6.59775 6.52105 6.37368
## Proportion of Variance 0.00478 0.00468 0.00461 0.00442 0.00423 0.00413 0.00394
## Cumulative Proportion  0.95299 0.95767 0.96227 0.96669 0.97092 0.97505 0.97899
##                          PC73    PC74    PC75    PC76   PC77    PC78   PC79
## Standard deviation     6.3405 6.27102 6.07648 5.78469 5.1714 4.60941 4.3017
## Proportion of Variance 0.0039 0.00382 0.00358 0.00325 0.0026 0.00206 0.0018
## Cumulative Proportion  0.9829 0.98671 0.99030 0.99354 0.9961 0.99820 1.0000
##                             PC80
## Standard deviation     1.709e-14
## Proportion of Variance 0.000e+00
## Cumulative Proportion  1.000e+00
autoplot(data.pca, data = data, colour = 'PAM50.mRNA') + ggtitle("PCA Analysis for all BC subtypes")

###T-SNE
data.tsne <- data
data.tsne_unique <- unique(data.tsne)
data.tsne <- as.matrix(data.tsne_unique[,32:length(data.tsne)])
set.seed(1)
data.tsne_out <- Rtsne(data.tsne, pca=FALSE, perplexity=1,dims=2, theta=0.5) # Run TSNE
summary(data.tsne_out$Y)
##        V1                V2         
##  Min.   :-83.756   Min.   :-82.975  
##  1st Qu.:-26.045   1st Qu.:-26.164  
##  Median : -1.118   Median :  7.204  
##  Mean   :  0.000   Mean   :  0.000  
##  3rd Qu.: 19.521   3rd Qu.: 23.574  
##  Max.   : 53.638   Max.   : 69.444
tsne_plot <- data.frame(x = data.tsne_out$Y[,1], y = data.tsne_out$Y[,2], col = data.tsne_unique$PAM50.mRNA) #TSNE plot
ggplot(tsne_plot) + geom_point(aes(x=x, y=y, color=col)) + ggtitle("T-SNE Analysis for all BC subtypes")

## Lasso Data ### Feature selection The Lasso regressions is used to select features introduced into the machine learning models.

###function to repeat lasso regression and return the selected model variables
lasso_sub=function(k=1, x_data, y_data) {
  set.seed(k)
  s=sample(nrow(data), size = 0.8*nrow(data))
  x_sub=x_data[s,]
  y_sub=y_data[s]
  model.sub=cv.glmnet(x=x_sub, y=y_sub, alpha=1, family='multinomial')
  coef.sub=coef(model.sub, s='lambda.1se')[-1]
  return(coef.sub)
}

options(warn = -1) #turn off warnings

###run model 100 times
niter=100
lasso.stab=sapply(1:niter, FUN = lasso_sub, x_data = as.matrix(data[,31:ncol(data)]), 
                  y_data=as.matrix(data[,21]))

###create a matrix of all predictor variables
lasso_matrix <- matrix(nrow=length(lasso.stab[[1]]),ncol=length(lasso.stab))
rownames(lasso_matrix) <- rownames(lasso.stab[[1]])
for (i in 1:300){ #loop through to put list contents into matrix
  lasso.data.frame <- as.matrix(lasso.stab[[i]])
  lasso_matrix[,i] <- lasso.data.frame
}
lasso_matrix <- ifelse(lasso_matrix != 0, 1, 0) #binary values 1/0 (selected/not selected)
lasso_matrix <- lasso_matrix[2:nrow(lasso_matrix),]
stable_variables <- as.data.frame(rowSums(lasso_matrix)) #data frame with count of how many times each variable is selected for a model
stable_variables$protein <- rownames(stable_variables) #column of variable names
colnames(stable_variables)[1] <- "times"
stable_variables <- stable_variables[!is.na(stable_variables$times),]  #remove NAs
stable_variables <- stable_variables[stable_variables$times != 0,] #remove all not selected variables
stable_variables <- stable_variables[order(-stable_variables$times),] #ordering by times 

Now let’s move on to the visualization of the first 50 proteins obtained by lasso regression.

###plotting 50 stable variables
(ggplot(stable_variables[1:50,], aes(x=reorder(as.factor(protein),-abs(times),mean), 
                                    y=times, col =reorder(as.factor(protein),-abs(times),mean), 
                                    fill =reorder(as.factor(protein),-abs(times),mean))) 
  + geom_col(show.legend = FALSE, alpha = 0.6) + theme(axis.text.x = element_text(angle = 90, hjust = 1), 
                                                       axis.text=element_text(size=10)) 
  + xlab("Protein ID") + ylab("Times selected")
  + ggtitle("Stable variables obtained by Lasso regression"))

stab_var <- stable_variables$protein[1:50] 
stab_var.ind <- which(colnames(data) %in% stab_var)

###boxplots for first 50 proteins obtained by lasso regression
plot_protein<- 1:length(stab_var[1:50])
plot_list <- list()
for (i in seq_along(plot_protein)){ 
  plot_list[[length(plot_list)+1]]  <- ggplot(data, aes_string("PAM50.mRNA", stab_var[i], col="PAM50.mRNA", fill="PAM50.mRNA")) + 
    geom_boxplot(alpha=0.3) + theme(axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank())
}
plot_grid(plotlist = plot_list,ncol = 1, nrow = 1) #only first one (in the BC_analysis you'll find the code for all)

###violin plots for first 50 proteins obtained by lasso regression
plot_protein<- 1:length(stab_var[1:50])
plot_list <- list()
for (i in seq_along(plot_protein)){ 
  plot_list[[length(plot_list)+1]]  <- ggplot(data, aes_string("PAM50.mRNA", stab_var[i], col="PAM50.mRNA", fill="PAM50.mRNA")) + 
    geom_violin(alpha=0.3) + geom_boxplot(width=0.1) + theme(axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank())
}
plot_grid(plotlist = plot_list,ncol = 1, nrow = 1) #only one (in the BC_analysis you'll find the code for all)

Using the biomaRt package, let’s create a csv file with 50 lasso proteins (gene ID, protein ID, description, times).

###create csv file with information about 50 proteins obtained by lasso regression 
library(biomaRt) #biomaRt database
listEnsembl()
biomart <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
searchAttributes(mart = biomart) #search attributes
getBM(attributes=c('external_gene_name','refseq_peptide','entrezgene_description'),filters='refseq_peptide',
      values=stab_var, mart=biomart)->stab_var.biomart # biomaRt query
stable_variables.50 <- stable_variables[1:50,]
filter(stable_variables.50, stable_variables.50$protein %in% stab_var.biomart$refseq_peptide) -> time
colnames(time) <- c('times_lassoRegression', 'refseq_peptide')
stab_var.biomart <- merge(stab_var.biomart, time, by.x = 'refseq_peptide')
stab_var.biomart[order(stab_var.biomart$times_lassoRegression, decreasing = TRUE), ] -> stab_var.biomart
#write.table(stab_var.biomart, "Lasso_proteins.csv", sep = ',', row.names = F)
print(stab_var.biomart)
##    refseq_peptide external_gene_name
## 44      NP_660208             SPATA5
## 26      NP_005970            S100A13
## 20      NP_004453              FDFT1
## 22      NP_004522              MOCS2
## 3    NP_001160163                TTK
## 9    NP_001258898           HSP90AB1
## 15      NP_003767             MRPL40
## 39      NP_542785              KRT72
## 35      NP_060866            METTL2B
## 18      NP_004388               DDX6
## 11      NP_002005              FKBP4
## 2    NP_001135891            MORF4L2
## 19      NP_004439              ERBB2
## 42      NP_653081             OSBPL2
## 36      NP_061170             TRIM36
## 43      NP_653304             LSM14B
## 17      NP_004243           SLC9A3R1
## 29      NP_038479               MYOF
## 14      NP_003212             TFAP2B
## 25      NP_005484             RANBP9
## 46      NP_848597               DTX3
## 16      NP_003875              KAT2B
## 4    NP_001171551              STAT6
## 12      NP_002677               PNMT
## 13      NP_003144              STAT6
## 7    NP_001229372               GRB7
## 23      NP_005130              ANXA3
## 32      NP_057164              GLOD4
## 38      NP_071739           C17orf75
## 40      NP_579899               MYOF
## 1    NP_001035492            DCUN1D4
## 48      NP_940869             RSBN1L
## 24      NP_005226              ERBB4
## 34      NP_060337               HPF1
## 6    NP_001186745               GGCT
## 21      NP_004499               IDI1
## 30      NP_055644              DDX46
## 31      NP_056513              GPKOW
## 45      NP_660344             TVP23C
## 8    NP_001257810             GNPDA2
## 37      NP_065821                CGN
## 5    NP_001186744               GGCT
## 27      NP_006345              TADA3
## 28      NP_006627             MTHFD2
## 33      NP_060182             PGPEP1
## 41      NP_579917              RAD17
## 47      NP_899229              PXDC1
## 10      NP_001371              DOCK1
##                                                                                  entrezgene_description
## 44                                                                         spermatogenesis associated 5
## 26                                                                     S100 calcium binding protein A13
## 20                                                           farnesyl-diphosphate farnesyltransferase 1
## 22                                                                      molybdenum cofactor synthesis 2
## 3                                                                                    TTK protein kinase
## 9                                                   heat shock protein 90 alpha family class B member 1
## 15                                                                  mitochondrial ribosomal protein L40
## 39                                                                                           keratin 72
## 35                                                                            methyltransferase like 2B
## 18                                                                                  DEAD-box helicase 6
## 11                                                                              FKBP prolyl isomerase 4
## 2                                                                             mortality factor 4 like 2
## 19                                                                    erb-b2 receptor tyrosine kinase 2
## 42                                                                     oxysterol binding protein like 2
## 36                                                                       tripartite motif containing 36
## 43                                                                                LSM family member 14B
## 17                                                                                   SLC9A3 regulator 1
## 29                                                                                            myoferlin
## 14                                                                       transcription factor AP-2 beta
## 25                                                                                RAN binding protein 9
## 46                                                                         deltex E3 ubiquitin ligase 3
## 16                                                                          lysine acetyltransferase 2B
## 4                                                    signal transducer and activator of transcription 6
## 12                                                               phenylethanolamine N-methyltransferase
## 13                                                   signal transducer and activator of transcription 6
## 7                                                                growth factor receptor bound protein 7
## 23                                                                                           annexin A3
## 32                                                                       glyoxalase domain containing 4
## 38                                                                  chromosome 17 open reading frame 75
## 40                                                                                            myoferlin
## 1                                                 defective in cullin neddylation 1 domain containing 4
## 48                                                                 round spermatid basic protein 1 like
## 24                                                                    erb-b2 receptor tyrosine kinase 4
## 34                                                                          histone PARylation factor 1
## 6                                                                        gamma-glutamylcyclotransferase
## 21                                                            isopentenyl-diphosphate delta isomerase 1
## 30                                                                                 DEAD-box helicase 46
## 31                                                                        G-patch domain and KOW motifs
## 45                                                     trans-golgi network vesicle protein 23 homolog C
## 8                                                                   glucosamine-6-phosphate deaminase 2
## 37                                                                                             cingulin
## 5                                                                        gamma-glutamylcyclotransferase
## 27                                                                            transcriptional adaptor 3
## 28 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase
## 33                                                                             pyroglutamyl-peptidase I
## 41                                                              RAD17 checkpoint clamp loader component
## 47                                                                               PX domain containing 1
## 10                                                                           dedicator of cytokinesis 1
##    times_lassoRegression
## 44                    77
## 26                    76
## 20                    75
## 22                    72
## 3                     69
## 9                     69
## 15                    69
## 39                    68
## 35                    59
## 18                    58
## 11                    54
## 2                     44
## 19                    44
## 42                    44
## 36                    42
## 43                    41
## 17                    39
## 29                    34
## 14                    32
## 25                    29
## 46                    29
## 16                    28
## 4                     27
## 12                    27
## 13                    23
## 7                     22
## 23                    22
## 32                    22
## 38                    21
## 40                    20
## 1                     18
## 48                    18
## 24                    16
## 34                    16
## 6                     15
## 21                    15
## 30                    15
## 31                    15
## 45                    15
## 8                     14
## 37                    14
## 5                     13
## 27                    13
## 28                    13
## 33                    13
## 41                    13
## 47                    13
## 10                    12

Creation the TRAIN and TEST data for Lasso data

  • 70% for TRAIN data
  • 30% for TEST data
###test and train split index
set.seed(1)
samp <- createDataPartition(data$PAM50.mRNA, p = 0.7, list = FALSE)
train_data <- data[samp, c(21, stab_var.ind)]
summary(train_data)
##   PAM50.mRNA          NP_579899         NP_038479        NP_001258898     
##  Length:59          Min.   :-3.9159   Min.   :-3.9159   Min.   :-1.44190  
##  Class :character   1st Qu.:-1.2782   1st Qu.:-1.2696   1st Qu.:-0.77219  
##  Mode  :character   Median :-0.6956   Median :-0.6863   Median : 0.06632  
##                     Mean   :-0.4095   Mean   :-0.4069   Mean   :-0.03541  
##                     3rd Qu.: 0.5315   3rd Qu.: 0.5448   3rd Qu.: 0.60987  
##                     Max.   : 3.7852   Max.   : 3.7852   Max.   : 1.69893  
##    NP_542785         NP_065821         NP_055644          NP_001371       
##  Min.   :-8.1930   Min.   :-5.2740   Min.   :-1.18100   Min.   :-2.28147  
##  1st Qu.:-1.7331   1st Qu.:-1.8230   1st Qu.:-0.36519   1st Qu.:-0.81302  
##  Median : 0.2807   Median :-0.8878   Median :-0.03887   Median : 0.04352  
##  Mean   :-0.1553   Mean   :-0.8216   Mean   :-0.02812   Mean   : 0.05964  
##  3rd Qu.: 1.9570   3rd Qu.: 0.1933   3rd Qu.: 0.25076   3rd Qu.: 0.66168  
##  Max.   : 5.1882   Max.   : 2.7069   Max.   : 1.02327   Max.   : 3.47779  
##    NP_002005        XP_003846537       NP_660208           NP_004439      
##  Min.   :-4.6254   Min.   :-1.1319   Min.   :-1.495747   Min.   :-5.8878  
##  1st Qu.:-1.9572   1st Qu.:-0.4568   1st Qu.:-0.493138   1st Qu.:-3.8998  
##  Median :-0.7818   Median :-0.2423   Median :-0.049677   Median :-2.5667  
##  Mean   :-0.7736   Mean   : 0.0467   Mean   :-0.008742   Mean   :-1.6350  
##  3rd Qu.: 0.3373   3rd Qu.: 0.4368   3rd Qu.: 0.434901   3rd Qu.:-0.7605  
##  Max.   : 3.4240   Max.   : 2.3366   Max.   : 1.657515   Max.   : 9.6682  
##    NP_005226         NP_004388         NP_001229372      NP_005130      
##  Min.   :-6.4647   Min.   :-1.47930   Min.   :-6.543   Min.   :-7.3499  
##  1st Qu.:-2.9787   1st Qu.:-0.34719   1st Qu.:-3.539   1st Qu.:-3.2954  
##  Median :-1.4884   Median :-0.05218   Median :-2.685   Median :-1.2813  
##  Mean   :-1.0411   Mean   : 0.09143   Mean   :-1.836   Mean   :-1.0504  
##  3rd Qu.: 0.1209   3rd Qu.: 0.69266   3rd Qu.:-1.169   3rd Qu.: 0.5383  
##  Max.   :10.4454   Max.   : 2.28696   Max.   : 8.979   Max.   : 6.3974  
##    NP_004243         NP_003144        NP_001171551       NP_072096      
##  Min.   :-3.9817   Min.   :-1.9798   Min.   :-1.9470   Min.   :-2.8719  
##  1st Qu.:-2.2748   1st Qu.:-0.4536   1st Qu.:-0.4483   1st Qu.:-0.5429  
##  Median :-1.3501   Median : 0.1147   Median : 0.1286   Median :-0.1055  
##  Mean   :-0.8537   Mean   : 0.1222   Mean   : 0.1215   Mean   :-0.1320  
##  3rd Qu.: 0.1430   3rd Qu.: 0.6768   3rd Qu.: 0.6616   3rd Qu.: 0.2997  
##  Max.   : 5.6714   Max.   : 2.8301   Max.   : 2.8140   Max.   : 1.1936  
##    NP_940869           NP_005484          NP_056513          NP_061170      
##  Min.   :-1.987365   Min.   :-1.50817   Min.   :-1.03743   Min.   :-3.5852  
##  1st Qu.:-0.475734   1st Qu.:-0.58139   1st Qu.:-0.41390   1st Qu.:-1.8435  
##  Median :-0.009813   Median :-0.05445   Median :-0.10664   Median :-1.0160  
##  Mean   :-0.060849   Mean   :-0.03572   Mean   :-0.05233   Mean   :-0.4868  
##  3rd Qu.: 0.401202   3rd Qu.: 0.44870   3rd Qu.: 0.19937   3rd Qu.: 0.5289  
##  Max.   : 1.471108   Max.   : 1.40462   Max.   : 1.29429   Max.   : 5.6897  
##    NP_653304         NP_653081          NP_057164         NP_006627      
##  Min.   :-4.2030   Min.   :-1.85269   Min.   :-1.8271   Min.   :-3.9493  
##  1st Qu.:-1.5728   1st Qu.:-0.56580   1st Qu.:-0.7193   1st Qu.:-1.7229  
##  Median :-0.6155   Median :-0.13410   Median : 0.1189   Median :-0.2343  
##  Mean   :-0.5083   Mean   : 0.03333   Mean   : 0.2121   Mean   :-0.2690  
##  3rd Qu.: 0.6527   3rd Qu.: 0.48876   3rd Qu.: 1.0657   3rd Qu.: 0.9709  
##  Max.   : 2.5448   Max.   : 3.62428   Max.   : 3.0124   Max.   : 3.8227  
##    NP_004453         NP_071739         NP_060337        NP_001186744     
##  Min.   :-4.1387   Min.   :-2.5815   Min.   :-1.5284   Min.   :-3.16931  
##  1st Qu.:-1.5544   1st Qu.:-0.8069   1st Qu.:-0.2767   1st Qu.:-0.96338  
##  Median :-0.3767   Median :-0.2152   Median : 0.1734   Median :-0.08595  
##  Mean   :-0.4027   Mean   :-0.1036   Mean   : 0.1794   Mean   : 0.01644  
##  3rd Qu.: 0.4646   3rd Qu.: 0.5228   3rd Qu.: 0.4522   3rd Qu.: 1.14623  
##  Max.   : 4.2437   Max.   : 2.4025   Max.   : 2.1870   Max.   : 3.64336  
##   NP_001186745       NP_001257810       NP_003212         NP_060866      
##  Min.   :-3.16931   Min.   :-1.6358   Min.   :-4.1699   Min.   :-2.5900  
##  1st Qu.:-0.96338   1st Qu.:-0.4878   1st Qu.:-1.2367   1st Qu.:-0.7931  
##  Median :-0.08595   Median : 0.1969   Median :-0.3767   Median :-0.3482  
##  Mean   : 0.01868   Mean   : 0.2720   Mean   :-0.4319   Mean   :-0.3493  
##  3rd Qu.: 1.14623   3rd Qu.: 0.9424   3rd Qu.: 0.5229   3rd Qu.: 0.1180  
##  Max.   : 3.64336   Max.   : 2.6328   Max.   : 2.2127   Max.   : 2.9262  
##   NP_001160163        NP_004499          NP_006345          NP_003875       
##  Min.   :-3.42211   Min.   :-2.94423   Min.   :-7.95438   Min.   :-4.15353  
##  1st Qu.:-1.18732   1st Qu.:-1.23316   1st Qu.:-0.57996   1st Qu.:-0.92176  
##  Median : 0.06316   Median : 0.18680   Median :-0.06555   Median : 0.04810  
##  Mean   : 0.02742   Mean   : 0.06117   Mean   :-0.28075   Mean   : 0.04303  
##  3rd Qu.: 0.91674   3rd Qu.: 0.94215   3rd Qu.: 0.27098   3rd Qu.: 0.83525  
##  Max.   : 2.89217   Max.   : 3.58994   Max.   : 2.41156   Max.   :11.75512  
##    NP_002677         NP_579917         NP_001135891       NP_004522      
##  Min.   :-11.361   Min.   :-4.98779   Min.   :-5.0503   Min.   :-2.3840  
##  1st Qu.: -8.368   1st Qu.:-0.77403   1st Qu.:-1.2707   1st Qu.:-1.0540  
##  Median : -7.081   Median :-0.09225   Median :-0.1240   Median :-0.4049  
##  Mean   : -5.811   Mean   :-0.26141   Mean   :-0.2037   Mean   :-0.2473  
##  3rd Qu.: -4.466   3rd Qu.: 0.47457   3rd Qu.: 0.5859   3rd Qu.: 0.5722  
##  Max.   : 10.216   Max.   : 1.69689   Max.   : 3.4142   Max.   : 2.8654  
##    NP_003767         NP_848597         NP_005970          NP_060182       
##  Min.   :-1.7319   Min.   :-3.9861   Min.   :-4.18213   Min.   :-3.15941  
##  1st Qu.:-0.5888   1st Qu.:-0.6245   1st Qu.:-1.41897   1st Qu.:-0.68303  
##  Median :-0.2699   Median : 0.2277   Median :-0.26626   Median : 0.20922  
##  Mean   :-0.1531   Mean   : 0.1859   Mean   : 0.08309   Mean   : 0.06945  
##  3rd Qu.: 0.3421   3rd Qu.: 1.0514   3rd Qu.: 1.60271   3rd Qu.: 0.94164  
##  Max.   : 2.1423   Max.   : 2.6558   Max.   : 5.16275   Max.   : 3.09499  
##   NP_001035492        NP_899229         NP_660344       
##  Min.   :-6.05108   Min.   :-4.0088   Min.   :-3.39489  
##  1st Qu.:-0.26050   1st Qu.:-0.2804   1st Qu.:-0.80112  
##  Median : 0.02385   Median : 0.2702   Median :-0.07568  
##  Mean   :-0.13957   Mean   : 0.3329   Mean   :-0.13958  
##  3rd Qu.: 0.67605   3rd Qu.: 1.2786   3rd Qu.: 0.59090  
##  Max.   : 2.08930   Max.   : 2.4978   Max.   : 4.21230
test_data <- data[-samp, c(21, stab_var.ind)]
summary(test_data)
##   PAM50.mRNA          NP_579899         NP_038479        NP_001258898     
##  Length:21          Min.   :-2.8493   Min.   :-2.8715   Min.   :-0.96268  
##  Class :character   1st Qu.:-1.5815   1st Qu.:-1.5667   1st Qu.:-0.70092  
##  Mode  :character   Median :-0.3341   Median :-0.3341   Median :-0.22428  
##                     Mean   :-0.4597   Mean   :-0.4596   Mean   :-0.06085  
##                     3rd Qu.: 0.6788   3rd Qu.: 0.6788   3rd Qu.: 0.40165  
##                     Max.   : 2.1070   Max.   : 2.0853   Max.   : 1.06645  
##    NP_542785        NP_065821         NP_055644          NP_001371       
##  Min.   :-8.644   Min.   :-5.0038   Min.   :-0.71531   Min.   :-1.65358  
##  1st Qu.:-3.268   1st Qu.:-1.5573   1st Qu.:-0.29045   1st Qu.:-0.89161  
##  Median :-1.406   Median :-0.7597   Median : 0.09215   Median : 0.25401  
##  Mean   :-1.370   Mean   :-0.9316   Mean   : 0.06150   Mean   : 0.03531  
##  3rd Qu.: 1.205   3rd Qu.: 0.3479   3rd Qu.: 0.33253   3rd Qu.: 0.63945  
##  Max.   : 2.629   Max.   : 1.7905   Max.   : 1.14505   Max.   : 1.41296  
##    NP_002005        XP_003846537        NP_660208         NP_004439     
##  Min.   :-2.7580   Min.   :-2.04227   Min.   :-1.1825   Min.   :-4.919  
##  1st Qu.:-1.1715   1st Qu.:-0.68125   1st Qu.:-0.4631   1st Qu.:-3.322  
##  Median :-0.4446   Median :-0.24366   Median : 0.0920   Median :-2.304  
##  Mean   :-0.3274   Mean   :-0.01299   Mean   : 0.1011   Mean   :-1.729  
##  3rd Qu.: 0.6306   3rd Qu.: 0.40006   3rd Qu.: 0.7408   3rd Qu.:-1.532  
##  Max.   : 2.2280   Max.   : 2.47057   Max.   : 1.2741   Max.   : 9.438  
##    NP_005226         NP_004388        NP_001229372      NP_005130      
##  Min.   :-5.3370   Min.   :-1.4118   Min.   :-6.963   Min.   :-8.8308  
##  1st Qu.:-2.6305   1st Qu.:-0.6526   1st Qu.:-4.030   1st Qu.:-4.2923  
##  Median :-1.7048   Median :-0.2659   Median :-2.164   Median :-2.3061  
##  Mean   :-0.7479   Mean   :-0.1973   Mean   :-1.937   Mean   :-2.3248  
##  3rd Qu.: 0.8890   3rd Qu.: 0.3494   3rd Qu.:-1.389   3rd Qu.:-0.6167  
##  Max.   : 9.7204   Max.   : 0.8814   Max.   : 8.965   Max.   : 3.5956  
##    NP_004243         NP_003144        NP_001171551        NP_072096       
##  Min.   :-4.3494   Min.   :-1.1524   Min.   :-1.14498   Min.   :-1.45482  
##  1st Qu.:-2.2135   1st Qu.:-0.1119   1st Qu.: 0.04338   1st Qu.:-0.58148  
##  Median :-1.0647   Median : 0.5646   Median : 0.56842   Median : 0.36236  
##  Mean   :-0.6237   Mean   : 0.3584   Mean   : 0.37775   Mean   : 0.05803  
##  3rd Qu.: 0.7448   3rd Qu.: 0.9051   3rd Qu.: 0.81561   3rd Qu.: 0.63145  
##  Max.   : 4.0709   Max.   : 1.8449   Max.   : 1.84490   Max.   : 1.14117  
##    NP_940869          NP_005484          NP_056513         NP_061170       
##  Min.   :-1.46208   Min.   :-1.05906   Min.   :-0.9638   Min.   :-4.71298  
##  1st Qu.:-0.42209   1st Qu.:-0.50315   1st Qu.:-0.5691   1st Qu.:-2.15915  
##  Median : 0.10605   Median :-0.28492   Median :-0.3914   Median :-1.56248  
##  Mean   : 0.03797   Mean   :-0.07778   Mean   :-0.2796   Mean   :-0.97732  
##  3rd Qu.: 0.55355   3rd Qu.: 0.07116   3rd Qu.:-0.1556   3rd Qu.:-0.06729  
##  Max.   : 1.37670   Max.   : 1.56246   Max.   : 1.3044   Max.   : 3.72464  
##    NP_653304           NP_653081         NP_057164          NP_006627      
##  Min.   :-2.996758   Min.   :-1.5026   Min.   :-1.92397   Min.   :-2.5320  
##  1st Qu.:-2.342573   1st Qu.:-0.4282   1st Qu.:-0.66416   1st Qu.:-1.7380  
##  Median :-1.273873   Median :-0.1973   Median :-0.28234   Median :-0.4650  
##  Mean   :-1.137436   Mean   :-0.1785   Mean   : 0.01943   Mean   :-0.4199  
##  3rd Qu.:-0.008532   3rd Qu.: 0.1819   3rd Qu.: 0.63751   3rd Qu.: 0.4291  
##  Max.   : 1.418603   Max.   : 0.9661   Max.   : 2.62671   Max.   : 2.5638  
##    NP_004453          NP_071739         NP_060337          NP_001186744     
##  Min.   :-3.22767   Min.   :-1.5383   Min.   :-0.667232   Min.   :-2.39120  
##  1st Qu.:-1.06796   1st Qu.:-0.7345   1st Qu.:-0.343704   1st Qu.:-0.70614  
##  Median :-0.39868   Median : 0.1818   Median :-0.119838   Median :-0.20813  
##  Mean   : 0.04539   Mean   : 0.2424   Mean   :-0.003719   Mean   :-0.01847  
##  3rd Qu.: 0.80457   3rd Qu.: 0.9296   3rd Qu.: 0.310813   3rd Qu.: 0.92664  
##  Max.   : 3.34544   Max.   : 2.4609   Max.   : 1.323088   Max.   : 2.58298  
##   NP_001186745       NP_001257810       NP_003212          NP_060866         
##  Min.   :-2.39120   Min.   :-1.2927   Min.   :-2.33411   Min.   :-1.3534381  
##  1st Qu.:-0.70614   1st Qu.:-0.2700   1st Qu.:-0.81516   1st Qu.:-0.5414421  
##  Median :-0.20813   Median : 0.3002   Median :-0.30052   Median :-0.2152410  
##  Mean   :-0.02104   Mean   : 0.4099   Mean   : 0.08917   Mean   :-0.0006818  
##  3rd Qu.: 0.92664   3rd Qu.: 0.7899   3rd Qu.: 1.25065   3rd Qu.: 0.4958501  
##  Max.   : 2.58298   Max.   : 2.1422   Max.   : 2.99862   Max.   : 2.4603584  
##   NP_001160163        NP_004499         NP_006345          NP_003875       
##  Min.   :-2.58103   Min.   :-3.5464   Min.   :-2.13172   Min.   :-4.97016  
##  1st Qu.:-0.46028   1st Qu.:-1.4284   1st Qu.:-0.75342   1st Qu.:-0.71044  
##  Median : 0.06316   Median :-0.5892   Median : 0.01263   Median : 0.04808  
##  Mean   :-0.20741   Mean   :-0.7853   Mean   :-0.01893   Mean   : 0.06236  
##  3rd Qu.: 0.06316   3rd Qu.: 0.2064   3rd Qu.: 0.59008   3rd Qu.: 1.05041  
##  Max.   : 1.97269   Max.   : 0.8233   Max.   : 2.76891   Max.   : 5.43255  
##    NP_002677         NP_579917        NP_001135891        NP_004522       
##  Min.   :-10.241   Min.   :-1.3528   Min.   :-1.74468   Min.   :-4.99686  
##  1st Qu.: -7.016   1st Qu.:-0.4171   1st Qu.:-0.96383   1st Qu.:-1.55870  
##  Median : -5.238   Median : 0.0139   Median :-0.41851   Median : 0.02322  
##  Mean   : -5.259   Mean   : 0.1787   Mean   :-0.22313   Mean   :-0.46001  
##  3rd Qu.: -3.911   3rd Qu.: 0.8614   3rd Qu.:-0.04714   3rd Qu.: 0.62059  
##  Max.   :  4.331   Max.   : 3.1893   Max.   : 3.17549   Max.   : 2.51056  
##    NP_003767          NP_848597         NP_005970         NP_060182      
##  Min.   :-1.87518   Min.   :-1.2668   Min.   :-3.7141   Min.   :-3.4672  
##  1st Qu.:-0.40798   1st Qu.:-0.5502   1st Qu.:-0.3587   1st Qu.:-0.5187  
##  Median : 0.06482   Median : 0.3744   Median : 0.3068   Median : 0.4353  
##  Mean   : 0.21708   Mean   : 0.6564   Mean   : 0.3944   Mean   : 0.6286  
##  3rd Qu.: 0.81882   3rd Qu.: 1.3331   3rd Qu.: 1.5019   3rd Qu.: 2.0368  
##  Max.   : 2.67788   Max.   : 3.2187   Max.   : 5.1614   Max.   : 3.8773  
##   NP_001035492       NP_899229          NP_660344       
##  Min.   :-4.5440   Min.   :-2.04346   Min.   :-4.12014  
##  1st Qu.:-1.0794   1st Qu.:-0.54677   1st Qu.:-0.70617  
##  Median :-0.2301   Median : 0.27018   Median :-0.07568  
##  Mean   :-0.4928   Mean   : 0.09408   Mean   :-0.18383  
##  3rd Qu.: 0.3235   3rd Qu.: 0.37805   3rd Qu.: 0.98085  
##  Max.   : 2.2644   Max.   : 2.72864   Max.   : 3.26007
###test and train data barplot
train_data.plot <- train_data
train_data.plot$data <- "train_data"
test_data.plot <- test_data
test_data.plot$data <- "test_data"
train_data.plot <- t(train_data.plot)
test_data.plot <- t(test_data.plot)
data.plot <- cbind.data.frame(train_data.plot,test_data.plot)
data.plot <- t(data.plot)
data.plot <- as.data.frame(data.plot)
ggplot(data.plot, aes(x=PAM50.mRNA, fill=data)) + geom_bar() +  ggtitle("train_data (0.7) and test_data (0.3) for Lasso proteins")

Models building for Lasso data

The three models were created for the Lasso data: * Support-Vector Machine * Random Forest * Neural Network Classifier

Support-Vector Machine

###Support-Vector Machine
set.seed(1)
train_control <- trainControl(method="repeatedcv", 
                              number=3, 
                              repeats=10, 
                              savePredictions = TRUE, 
                              summaryFunction = multiClassSummary) #settng up train control for cross validation and calibration of hyperparameter
grid <- expand.grid(C = seq(0.000001,0.15,0.002)) #Tunegrid for different values of C
set.seed(1)
svm.lin.mod <- train(PAM50.mRNA ~ ., 
                     data=train_data, 
                     trControl=train_control, 
                     method="svmLinear", 
                     preProcess = c("center","scale"), 
                     tuneGrid =grid, 
                     tuneLength = 10) #training
svm.predicts <- predict(svm.lin.mod, 
                        newdata = test_data) #Creating predictions on test set
confusionMatrix(svm.predicts, as.factor(test_data$PAM50.mRNA)) #confusion matrix
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             5             1         0         0
##   HER2-enriched          0             2         0         0
##   Luminal A              0             0         6         1
##   Luminal B              0             0         0         6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.9048          
##                  95% CI : (0.6962, 0.9883)
##     No Information Rate : 0.3333          
##     P-Value [Acc > NIR] : 8.441e-08       
##                                           
##                   Kappa : 0.8692          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     1.0000              0.66667           1.0000
## Specificity                     0.9375              1.00000           0.9333
## Pos Pred Value                  0.8333              1.00000           0.8571
## Neg Pred Value                  1.0000              0.94737           1.0000
## Prevalence                      0.2381              0.14286           0.2857
## Detection Rate                  0.2381              0.09524           0.2857
## Detection Prevalence            0.2857              0.09524           0.3333
## Balanced Accuracy               0.9688              0.83333           0.9667
##                      Class: Luminal B
## Sensitivity                    0.8571
## Specificity                    1.0000
## Pos Pred Value                 1.0000
## Neg Pred Value                 0.9333
## Prevalence                     0.3333
## Detection Rate                 0.2857
## Detection Prevalence           0.2857
## Balanced Accuracy              0.9286

Random Forest

set.seed(1)
random.forest.mod <- randomForest(as.factor(PAM50.mRNA) ~ ., 
                                  data=train_data, 
                                  ntree = 500, 
                                  mtry = 8, 
                                  importance = TRUE) #training
plot(random.forest.mod)

random.forest.predicts <- predict(random.forest.mod, newdata=test_data, type = "class") #prediction
confusionMatrix(random.forest.predicts, as.factor(test_data$PAM50.mRNA)) #confusion matrix
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             4             1         0         0
##   HER2-enriched          0             2         0         0
##   Luminal A              1             0         6         1
##   Luminal B              0             0         0         6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.8571          
##                  95% CI : (0.6366, 0.9695)
##     No Information Rate : 0.3333          
##     P-Value [Acc > NIR] : 1.102e-06       
##                                           
##                   Kappa : 0.8031          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     0.8000              0.66667           1.0000
## Specificity                     0.9375              1.00000           0.8667
## Pos Pred Value                  0.8000              1.00000           0.7500
## Neg Pred Value                  0.9375              0.94737           1.0000
## Prevalence                      0.2381              0.14286           0.2857
## Detection Rate                  0.1905              0.09524           0.2857
## Detection Prevalence            0.2381              0.09524           0.3810
## Balanced Accuracy               0.8688              0.83333           0.9333
##                      Class: Luminal B
## Sensitivity                    0.8571
## Specificity                    1.0000
## Pos Pred Value                 1.0000
## Neg Pred Value                 0.9333
## Prevalence                     0.3333
## Detection Rate                 0.2857
## Detection Prevalence           0.2857
## Balanced Accuracy              0.9286

Neural Network Classifier

neural.network.mod <-neuralnet(as.factor(PAM50.mRNA) ~ .,          
                               data=train_data, 
                               hidden = c(30, 15, 8), 
                               linear.output = FALSE,
                               act.fct = "logistic",
                               algorithm = 'sag')
plot(neural.network.mod,
     intercept = F,
     rep = 'best',
     col.hidden = 'darkblue', 
     col.hidden.synapse = 'black', 
     show.weights = F, 
     fill = 'lightblue',
     col.intercept  = 'red',
     fontsize = 8, 
     dimension = 15)

neural.network.mod$result.matrix #errors for model
##                                    [,1]
## error                       0.021195932
## reached.threshold           0.009638026
## steps                      28.000000000
## Intercept.to.1layhid1       0.785549086
## NP_579899.to.1layhid1      -0.262016110
## NP_038479.to.1layhid1      -1.225498153
## NP_001258898.to.1layhid1    1.919385529
## NP_542785.to.1layhid1      -0.001976054
## NP_065821.to.1layhid1       0.814236843
## NP_055644.to.1layhid1      -0.085401380
## NP_001371.to.1layhid1      -0.444148855
## NP_002005.to.1layhid1       0.494588215
## XP_003846537.to.1layhid1   -0.720745768
## NP_660208.to.1layhid1       0.181616660
## NP_004439.to.1layhid1      -3.002664943
## NP_005226.to.1layhid1      -0.593684137
## NP_004388.to.1layhid1       1.249560671
## NP_001229372.to.1layhid1    0.297049597
## NP_005130.to.1layhid1      -1.310970062
## NP_004243.to.1layhid1      -1.082917284
## NP_003144.to.1layhid1      -0.063720981
## NP_001171551.to.1layhid1   -0.352858707
## NP_072096.to.1layhid1       0.651974432
## NP_940869.to.1layhid1       0.073908843
## NP_005484.to.1layhid1       1.878393721
## NP_056513.to.1layhid1       0.953121334
## NP_061170.to.1layhid1       0.045991665
## NP_653304.to.1layhid1       1.357147715
## NP_653081.to.1layhid1       3.077741810
## NP_057164.to.1layhid1      -1.525861891
## NP_006627.to.1layhid1       0.459609912
## NP_004453.to.1layhid1       0.570314802
## NP_071739.to.1layhid1       1.739661195
## NP_060337.to.1layhid1       0.526376418
## NP_001186744.to.1layhid1    0.550308074
## NP_001186745.to.1layhid1    2.186505047
## NP_001257810.to.1layhid1   -1.299257031
## NP_003212.to.1layhid1      -2.371503709
## NP_060866.to.1layhid1      -0.161453527
## NP_001160163.to.1layhid1    0.491848755
## NP_004499.to.1layhid1       2.295899501
## NP_006345.to.1layhid1       2.462965208
## NP_003875.to.1layhid1      -0.798802500
## NP_002677.to.1layhid1      -1.669845876
## NP_579917.to.1layhid1      -0.631330868
## NP_001135891.to.1layhid1    0.572934776
## NP_004522.to.1layhid1       0.892971088
## NP_003767.to.1layhid1       2.406895945
## NP_848597.to.1layhid1       0.482211035
## NP_005970.to.1layhid1       0.132082885
## NP_060182.to.1layhid1      -1.166360695
## NP_001035492.to.1layhid1    0.349673129
## NP_899229.to.1layhid1       0.317924649
## NP_660344.to.1layhid1      -0.341541938
## Intercept.to.1layhid2       0.153659284
## NP_579899.to.1layhid2      -1.115550579
## NP_038479.to.1layhid2       0.349364804
## NP_001258898.to.1layhid2   -0.052976450
## NP_542785.to.1layhid2       0.056010592
## NP_065821.to.1layhid2       1.452301335
## NP_055644.to.1layhid2      -0.210892174
## NP_001371.to.1layhid2       0.664658551
## NP_002005.to.1layhid2      -0.190933711
## XP_003846537.to.1layhid2   -1.017669586
## NP_660208.to.1layhid2      -1.379904641
## NP_004439.to.1layhid2       0.232814426
## NP_005226.to.1layhid2       3.000005549
## NP_004388.to.1layhid2       1.169568357
## NP_001229372.to.1layhid2    1.685611153
## NP_005130.to.1layhid2       1.027092175
## NP_004243.to.1layhid2       1.190725944
## NP_003144.to.1layhid2       0.078017961
## NP_001171551.to.1layhid2    0.191204760
## NP_072096.to.1layhid2       0.520591080
## NP_940869.to.1layhid2       1.480275582
## NP_005484.to.1layhid2       1.960523521
## NP_056513.to.1layhid2       0.552770921
## NP_061170.to.1layhid2      -0.702950827
## NP_653304.to.1layhid2      -1.243611585
## NP_653081.to.1layhid2      -1.138990591
## NP_057164.to.1layhid2       0.736797004
## NP_006627.to.1layhid2       0.655825172
## NP_004453.to.1layhid2       0.218792369
## NP_071739.to.1layhid2      -1.526026033
## NP_060337.to.1layhid2      -1.068150679
## NP_001186744.to.1layhid2    0.198913657
## NP_001186745.to.1layhid2   -1.434851099
## NP_001257810.to.1layhid2   -0.657795339
## NP_003212.to.1layhid2      -0.706347641
## NP_060866.to.1layhid2      -0.332845024
## NP_001160163.to.1layhid2    0.150365282
## NP_004499.to.1layhid2      -1.860642089
## NP_006345.to.1layhid2       1.097909116
## NP_003875.to.1layhid2      -0.714654576
## NP_002677.to.1layhid2       0.196793129
## NP_579917.to.1layhid2      -0.218729027
## NP_001135891.to.1layhid2   -1.982626388
## NP_004522.to.1layhid2       1.515779176
## NP_003767.to.1layhid2      -0.761072639
## NP_848597.to.1layhid2       0.987991075
## NP_005970.to.1layhid2       1.844163589
## NP_060182.to.1layhid2       1.027236602
## NP_001035492.to.1layhid2    0.143315800
## NP_899229.to.1layhid2      -1.353909235
## NP_660344.to.1layhid2       1.942546902
## Intercept.to.1layhid3       2.010387776
## NP_579899.to.1layhid3       0.220609340
## NP_038479.to.1layhid3       1.459623930
## NP_001258898.to.1layhid3   -1.258171669
## NP_542785.to.1layhid3      -0.241613528
## NP_065821.to.1layhid3       2.227261873
## NP_055644.to.1layhid3       0.777774937
## NP_001371.to.1layhid3       0.531872178
## NP_002005.to.1layhid3      -0.491435931
## XP_003846537.to.1layhid3    0.496558195
## NP_660208.to.1layhid3      -1.049419687
## NP_004439.to.1layhid3      -0.120515164
## NP_005226.to.1layhid3       0.741990117
## NP_004388.to.1layhid3      -0.749947622
## NP_001229372.to.1layhid3    0.769647954
## NP_005130.to.1layhid3       0.842882408
## NP_004243.to.1layhid3      -0.518941086
## NP_003144.to.1layhid3       0.253185799
## NP_001171551.to.1layhid3    1.241267680
## NP_072096.to.1layhid3       2.416360441
## NP_940869.to.1layhid3       2.238629110
## NP_005484.to.1layhid3       1.181589250
## NP_056513.to.1layhid3      -1.324020494
## NP_061170.to.1layhid3       0.470210255
## NP_653304.to.1layhid3      -0.425291700
## NP_653081.to.1layhid3       1.391175302
## NP_057164.to.1layhid3       0.230867624
## NP_006627.to.1layhid3       2.523091056
## NP_004453.to.1layhid3       0.293908063
## NP_071739.to.1layhid3      -0.814738390
## NP_060337.to.1layhid3      -0.434233737
## NP_001186744.to.1layhid3   -0.971688598
## NP_001186745.to.1layhid3   -0.387916032
## NP_001257810.to.1layhid3    1.485872857
## NP_003212.to.1layhid3       0.312407973
## NP_060866.to.1layhid3      -2.389670223
## NP_001160163.to.1layhid3   -1.545273761
## NP_004499.to.1layhid3       0.012979751
## NP_006345.to.1layhid3      -0.755606287
## NP_003875.to.1layhid3       0.260279346
## NP_002677.to.1layhid3      -0.328927103
## NP_579917.to.1layhid3      -0.336599699
## NP_001135891.to.1layhid3    1.331651020
## NP_004522.to.1layhid3      -0.867530131
## NP_003767.to.1layhid3      -0.859139174
## NP_848597.to.1layhid3       0.539231746
## NP_005970.to.1layhid3      -0.302648750
## NP_060182.to.1layhid3       0.048547855
## NP_001035492.to.1layhid3    0.422142918
## NP_899229.to.1layhid3       0.985977458
## NP_660344.to.1layhid3       0.173539700
## Intercept.to.1layhid4       2.105763051
## NP_579899.to.1layhid4       0.888595374
## NP_038479.to.1layhid4       0.187842708
## NP_001258898.to.1layhid4   -1.156950445
## NP_542785.to.1layhid4       1.793476891
## NP_065821.to.1layhid4       0.213197347
## NP_055644.to.1layhid4       1.819541211
## NP_001371.to.1layhid4       3.428527481
## NP_002005.to.1layhid4      -0.150050339
## XP_003846537.to.1layhid4    0.577702113
## NP_660208.to.1layhid4      -1.034157822
## NP_004439.to.1layhid4       0.325376633
## NP_005226.to.1layhid4       0.187672012
## NP_004388.to.1layhid4      -0.488623655
## NP_001229372.to.1layhid4    0.861144681
## NP_005130.to.1layhid4      -0.825941559
## NP_004243.to.1layhid4       0.754556398
## NP_003144.to.1layhid4       0.317830928
## NP_001171551.to.1layhid4   -1.110820029
## NP_072096.to.1layhid4       0.192079082
## NP_940869.to.1layhid4      -2.597219104
## NP_005484.to.1layhid4      -1.107636461
## NP_056513.to.1layhid4       1.467835025
## NP_061170.to.1layhid4      -0.585686476
## NP_653304.to.1layhid4       0.216149587
## NP_653081.to.1layhid4       0.694102984
## NP_057164.to.1layhid4      -1.672286149
## NP_006627.to.1layhid4      -1.346039664
## NP_004453.to.1layhid4      -0.836338886
## NP_071739.to.1layhid4       0.581690992
## NP_060337.to.1layhid4       0.640629065
## NP_001186744.to.1layhid4    2.159846161
## NP_001186745.to.1layhid4   -1.274042802
## NP_001257810.to.1layhid4    0.537127472
## NP_003212.to.1layhid4       0.201428065
## NP_060866.to.1layhid4      -0.533256349
## NP_001160163.to.1layhid4   -1.696287452
## NP_004499.to.1layhid4       0.100376974
## NP_006345.to.1layhid4       1.420584843
## NP_003875.to.1layhid4       0.238651391
## NP_002677.to.1layhid4       0.640585516
## NP_579917.to.1layhid4      -0.965578829
## NP_001135891.to.1layhid4   -0.208501733
## NP_004522.to.1layhid4      -1.372900354
## NP_003767.to.1layhid4       0.588739145
## NP_848597.to.1layhid4      -0.665966563
## NP_005970.to.1layhid4       0.819133366
## NP_060182.to.1layhid4       0.473178684
## NP_001035492.to.1layhid4   -0.214700332
## NP_899229.to.1layhid4       0.455600547
## NP_660344.to.1layhid4      -0.700919565
## Intercept.to.1layhid5       0.221588354
## NP_579899.to.1layhid5       1.490748329
## NP_038479.to.1layhid5       2.087952557
## NP_001258898.to.1layhid5    0.033472855
## NP_542785.to.1layhid5      -1.396237853
## NP_065821.to.1layhid5       0.788251524
## NP_055644.to.1layhid5       0.641770027
## NP_001371.to.1layhid5      -0.067084215
## NP_002005.to.1layhid5       0.281368265
## XP_003846537.to.1layhid5   -0.870438186
## NP_660208.to.1layhid5      -0.169932939
## NP_004439.to.1layhid5       0.684411005
## NP_005226.to.1layhid5       1.006243765
## NP_004388.to.1layhid5      -1.597080737
## NP_001229372.to.1layhid5    0.437167630
## NP_005130.to.1layhid5      -2.222086068
## NP_004243.to.1layhid5       1.919762002
## NP_003144.to.1layhid5      -0.393831195
## NP_001171551.to.1layhid5    0.313414992
## NP_072096.to.1layhid5      -2.610913274
## NP_940869.to.1layhid5       1.011959329
## NP_005484.to.1layhid5      -1.908923937
## NP_056513.to.1layhid5      -0.610032337
## NP_061170.to.1layhid5       0.232277198
## NP_653304.to.1layhid5      -1.967113734
## NP_653081.to.1layhid5      -0.831606989
## NP_057164.to.1layhid5      -0.626790047
## NP_006627.to.1layhid5      -0.068025777
## NP_004453.to.1layhid5      -1.448368405
## NP_071739.to.1layhid5      -0.648634899
## NP_060337.to.1layhid5       1.945307832
## NP_001186744.to.1layhid5    0.200367689
## NP_001186745.to.1layhid5    0.103825839
## NP_001257810.to.1layhid5   -1.026237499
## NP_003212.to.1layhid5       1.176626956
## NP_060866.to.1layhid5       0.447625184
## NP_001160163.to.1layhid5   -1.126065753
## NP_004499.to.1layhid5      -0.497150285
## NP_006345.to.1layhid5      -0.094664946
## NP_003875.to.1layhid5       0.269432209
## NP_002677.to.1layhid5       0.214620469
## NP_579917.to.1layhid5      -0.184251160
## NP_001135891.to.1layhid5    0.552614128
## NP_004522.to.1layhid5      -0.819810345
## NP_003767.to.1layhid5       0.083709134
## NP_848597.to.1layhid5      -1.179020907
## NP_005970.to.1layhid5       1.280424339
## NP_060182.to.1layhid5       0.111220322
## NP_001035492.to.1layhid5    0.530210390
## NP_899229.to.1layhid5      -0.502996752
## NP_660344.to.1layhid5       3.096018559
## Intercept.to.1layhid6      -0.472307306
## NP_579899.to.1layhid6      -1.138156957
## NP_038479.to.1layhid6      -0.014292442
## NP_001258898.to.1layhid6   -0.829683371
## NP_542785.to.1layhid6      -0.869143541
## NP_065821.to.1layhid6      -1.275165612
## NP_055644.to.1layhid6       0.460092869
## NP_001371.to.1layhid6      -1.640873646
## NP_002005.to.1layhid6      -0.741935492
## XP_003846537.to.1layhid6    0.693233859
## NP_660208.to.1layhid6       2.718769443
## NP_004439.to.1layhid6      -0.728451794
## NP_005226.to.1layhid6       0.531629449
## NP_004388.to.1layhid6       0.470977371
## NP_001229372.to.1layhid6   -0.151536567
## NP_005130.to.1layhid6      -0.073636147
## NP_004243.to.1layhid6       0.730935745
## NP_003144.to.1layhid6       0.392122469
## NP_001171551.to.1layhid6    0.630768238
## NP_072096.to.1layhid6       2.098831934
## NP_940869.to.1layhid6       0.986247798
## NP_005484.to.1layhid6      -0.406973374
## NP_056513.to.1layhid6       1.105194880
## NP_061170.to.1layhid6      -0.198696445
## NP_653304.to.1layhid6      -2.093517388
## NP_653081.to.1layhid6      -1.311033055
## NP_057164.to.1layhid6      -0.602191920
## NP_006627.to.1layhid6      -3.699763169
## NP_004453.to.1layhid6      -1.751814701
## NP_071739.to.1layhid6       0.469625476
## NP_060337.to.1layhid6       1.664865979
## NP_001186744.to.1layhid6   -0.246470091
## NP_001186745.to.1layhid6    0.140087034
## NP_001257810.to.1layhid6    0.889248850
## NP_003212.to.1layhid6      -1.065748446
## NP_060866.to.1layhid6      -0.132518279
## NP_001160163.to.1layhid6    1.730843128
## NP_004499.to.1layhid6       0.377013730
## NP_006345.to.1layhid6       0.405434726
## NP_003875.to.1layhid6       0.489386932
## NP_002677.to.1layhid6      -0.763065994
## NP_579917.to.1layhid6       0.928361962
## NP_001135891.to.1layhid6    0.506678368
## NP_004522.to.1layhid6      -0.299351049
## NP_003767.to.1layhid6      -1.284318461
## NP_848597.to.1layhid6      -2.207869249
## NP_005970.to.1layhid6      -0.227243625
## NP_060182.to.1layhid6       1.210399515
## NP_001035492.to.1layhid6    1.265561076
## NP_899229.to.1layhid6      -0.145679498
## NP_660344.to.1layhid6       0.786628200
## Intercept.to.1layhid7       1.645637303
## NP_579899.to.1layhid7       0.007869461
## NP_038479.to.1layhid7       0.894989603
## NP_001258898.to.1layhid7   -0.883762985
## NP_542785.to.1layhid7      -0.846659367
## NP_065821.to.1layhid7      -0.021673964
## NP_055644.to.1layhid7       1.109024346
## NP_001371.to.1layhid7      -1.287247295
## NP_002005.to.1layhid7       0.982770387
## XP_003846537.to.1layhid7   -1.339339120
## NP_660208.to.1layhid7      -0.449120336
## NP_004439.to.1layhid7       0.569036853
## NP_005226.to.1layhid7      -0.440847220
## NP_004388.to.1layhid7       0.211478134
## NP_001229372.to.1layhid7    1.299469050
## NP_005130.to.1layhid7       0.140985583
## NP_004243.to.1layhid7       0.699957325
## NP_003144.to.1layhid7       1.152735649
## NP_001171551.to.1layhid7   -2.582666407
## NP_072096.to.1layhid7      -0.158896108
## NP_940869.to.1layhid7      -0.280955383
## NP_005484.to.1layhid7      -1.674685458
## NP_056513.to.1layhid7      -0.201617487
## NP_061170.to.1layhid7       2.463164283
## NP_653304.to.1layhid7      -0.031647314
## NP_653081.to.1layhid7      -0.536613113
## NP_057164.to.1layhid7       0.968235842
## NP_006627.to.1layhid7       2.795446812
## NP_004453.to.1layhid7       0.112870562
## NP_071739.to.1layhid7       0.203169041
## NP_060337.to.1layhid7       0.627238944
## NP_001186744.to.1layhid7    0.002571206
## NP_001186745.to.1layhid7   -0.696141669
## NP_001257810.to.1layhid7    0.863183287
## NP_003212.to.1layhid7      -0.494700744
## NP_060866.to.1layhid7       0.402202452
## NP_001160163.to.1layhid7   -0.492918937
## NP_004499.to.1layhid7      -0.610251480
## NP_006345.to.1layhid7       0.069733904
## NP_003875.to.1layhid7       0.753393939
## NP_002677.to.1layhid7      -0.387421977
## NP_579917.to.1layhid7      -1.300223721
## NP_001135891.to.1layhid7    2.059020307
## NP_004522.to.1layhid7       0.706446205
## NP_003767.to.1layhid7       0.833611326
## NP_848597.to.1layhid7      -1.374478259
## NP_005970.to.1layhid7       0.083503177
## NP_060182.to.1layhid7       0.448333835
## NP_001035492.to.1layhid7   -1.740023938
## NP_899229.to.1layhid7      -1.503380204
## NP_660344.to.1layhid7      -0.097484644
## Intercept.to.1layhid8      -0.430977408
## NP_579899.to.1layhid8      -1.191790821
## NP_038479.to.1layhid8      -2.996542102
## NP_001258898.to.1layhid8   -1.795300315
## NP_542785.to.1layhid8      -0.621785273
## NP_065821.to.1layhid8       1.188506578
## NP_055644.to.1layhid8       1.778791995
## NP_001371.to.1layhid8       1.516034059
## NP_002005.to.1layhid8      -1.051059199
## XP_003846537.to.1layhid8   -1.813024045
## NP_660208.to.1layhid8       1.712864483
## NP_004439.to.1layhid8      -0.683226814
## NP_005226.to.1layhid8       1.978186965
## NP_004388.to.1layhid8       1.259586857
## NP_001229372.to.1layhid8    0.887739581
## NP_005130.to.1layhid8       0.215870246
## NP_004243.to.1layhid8       0.587260481
## NP_003144.to.1layhid8      -1.502765625
## NP_001171551.to.1layhid8   -2.113355873
## NP_072096.to.1layhid8       1.600487134
## NP_940869.to.1layhid8       1.008916891
## NP_005484.to.1layhid8       1.057599333
## NP_056513.to.1layhid8      -0.120150838
## NP_061170.to.1layhid8       0.788408447
## NP_653304.to.1layhid8      -0.074597882
## NP_653081.to.1layhid8       0.599038237
## NP_057164.to.1layhid8      -0.794287800
## NP_006627.to.1layhid8      -0.203023439
## NP_004453.to.1layhid8       0.395047039
## NP_071739.to.1layhid8       0.917811313
## NP_060337.to.1layhid8      -1.206822306
## NP_001186744.to.1layhid8   -1.082878790
## NP_001186745.to.1layhid8   -0.590623127
## NP_001257810.to.1layhid8   -0.814561859
## NP_003212.to.1layhid8      -0.012298071
## NP_060866.to.1layhid8       1.716958715
## NP_001160163.to.1layhid8    3.142406474
## NP_004499.to.1layhid8       2.059252223
## NP_006345.to.1layhid8       1.692464402
## NP_003875.to.1layhid8      -1.109996868
## NP_002677.to.1layhid8      -1.885930810
## NP_579917.to.1layhid8      -0.667631979
## NP_001135891.to.1layhid8    1.558142363
## NP_004522.to.1layhid8       1.582605033
## NP_003767.to.1layhid8      -0.506277748
## NP_848597.to.1layhid8      -1.297606969
## NP_005970.to.1layhid8      -1.498930799
## NP_060182.to.1layhid8       0.196660410
## NP_001035492.to.1layhid8    1.683982905
## NP_899229.to.1layhid8       0.063136744
## NP_660344.to.1layhid8      -2.105325318
## Intercept.to.1layhid9       0.220407411
## NP_579899.to.1layhid9       0.097094678
## NP_038479.to.1layhid9      -0.271185497
## NP_001258898.to.1layhid9   -1.246745851
## NP_542785.to.1layhid9      -0.805621076
## NP_065821.to.1layhid9      -1.280506530
## NP_055644.to.1layhid9       1.625626423
## NP_001371.to.1layhid9       0.246382836
## NP_002005.to.1layhid9      -0.467134288
## XP_003846537.to.1layhid9    2.279925570
## NP_660208.to.1layhid9       0.853709676
## NP_004439.to.1layhid9      -0.338553163
## NP_005226.to.1layhid9       3.063121231
## NP_004388.to.1layhid9      -0.791699820
## NP_001229372.to.1layhid9   -1.378075498
## NP_005130.to.1layhid9      -1.594672842
## NP_004243.to.1layhid9       0.335157499
## NP_003144.to.1layhid9       0.156661226
## NP_001171551.to.1layhid9   -0.242762142
## NP_072096.to.1layhid9       0.423406313
## NP_940869.to.1layhid9       0.367948989
## NP_005484.to.1layhid9       1.024066873
## NP_056513.to.1layhid9       0.571192722
## NP_061170.to.1layhid9       0.042210736
## NP_653304.to.1layhid9      -2.536304262
## NP_653081.to.1layhid9      -1.189819378
## NP_057164.to.1layhid9       1.792936680
## NP_006627.to.1layhid9       0.676789519
## NP_004453.to.1layhid9      -0.604734402
## NP_071739.to.1layhid9       0.072645896
## NP_060337.to.1layhid9      -0.587656088
## NP_001186744.to.1layhid9    0.298094389
## NP_001186745.to.1layhid9    2.559499832
## NP_001257810.to.1layhid9    0.502892017
## NP_003212.to.1layhid9      -0.312501680
## NP_060866.to.1layhid9       0.864005988
## NP_001160163.to.1layhid9   -0.003900838
## NP_004499.to.1layhid9       0.029424753
## NP_006345.to.1layhid9      -0.727074271
## NP_003875.to.1layhid9      -1.051550460
## NP_002677.to.1layhid9      -0.759748041
## NP_579917.to.1layhid9       0.467299381
## NP_001135891.to.1layhid9    0.390124953
## NP_004522.to.1layhid9      -0.014196600
## NP_003767.to.1layhid9      -0.615884662
## NP_848597.to.1layhid9      -0.012712903
## NP_005970.to.1layhid9       1.750527867
## NP_060182.to.1layhid9       1.184790385
## NP_001035492.to.1layhid9   -0.765675343
## NP_899229.to.1layhid9       0.418689342
## NP_660344.to.1layhid9      -1.001356908
## Intercept.to.1layhid10      0.220940923
## NP_579899.to.1layhid10      1.857742377
## NP_038479.to.1layhid10      0.916307668
## NP_001258898.to.1layhid10  -2.041723538
## NP_542785.to.1layhid10      1.962425779
## NP_065821.to.1layhid10     -0.434193031
## NP_055644.to.1layhid10      0.082442154
## NP_001371.to.1layhid10      0.464026368
## NP_002005.to.1layhid10     -0.558694942
## XP_003846537.to.1layhid10  -1.280787572
## NP_660208.to.1layhid10     -1.148388076
## NP_004439.to.1layhid10      0.365222260
## NP_005226.to.1layhid10      0.000774153
## NP_004388.to.1layhid10     -1.853150837
## NP_001229372.to.1layhid10  -0.537508942
## NP_005130.to.1layhid10      0.362429513
## NP_004243.to.1layhid10     -0.648715576
## NP_003144.to.1layhid10      1.763818829
## NP_001171551.to.1layhid10   0.132458201
## NP_072096.to.1layhid10      0.087676030
## NP_940869.to.1layhid10     -0.848539644
## NP_005484.to.1layhid10     -0.188378391
## NP_056513.to.1layhid10     -1.433027119
## NP_061170.to.1layhid10      0.093026122
## NP_653304.to.1layhid10      1.904299678
## NP_653081.to.1layhid10     -1.896135886
## NP_057164.to.1layhid10      1.056062137
## NP_006627.to.1layhid10     -0.654325686
## NP_004453.to.1layhid10     -0.838383084
## NP_071739.to.1layhid10     -1.173254755
## NP_060337.to.1layhid10     -1.354488032
## NP_001186744.to.1layhid10  -1.934044386
## NP_001186745.to.1layhid10  -0.527964140
## NP_001257810.to.1layhid10  -0.463637372
## NP_003212.to.1layhid10      1.000130064
## NP_060866.to.1layhid10     -1.607915497
## NP_001160163.to.1layhid10   0.939287804
## NP_004499.to.1layhid10      0.615983609
## NP_006345.to.1layhid10     -0.718462044
## NP_003875.to.1layhid10     -0.159574713
## NP_002677.to.1layhid10     -0.529384807
## NP_579917.to.1layhid10     -0.234379062
## NP_001135891.to.1layhid10  -0.985666453
## NP_004522.to.1layhid10     -0.911212060
## NP_003767.to.1layhid10      0.879255926
## NP_848597.to.1layhid10     -0.417453996
## NP_005970.to.1layhid10      0.309582232
## NP_060182.to.1layhid10     -0.517444722
## NP_001035492.to.1layhid10  -0.072913256
## NP_899229.to.1layhid10     -0.370837217
## NP_660344.to.1layhid10      0.825694880
## Intercept.to.1layhid11      0.073578934
## NP_579899.to.1layhid11      2.268292435
## NP_038479.to.1layhid11     -1.387758092
## NP_001258898.to.1layhid11   0.342460951
## NP_542785.to.1layhid11     -0.266459348
## NP_065821.to.1layhid11     -0.347897835
## NP_055644.to.1layhid11     -0.844515715
## NP_001371.to.1layhid11     -2.205184453
## NP_002005.to.1layhid11     -2.055000652
## XP_003846537.to.1layhid11  -0.961348757
## NP_660208.to.1layhid11      0.120443496
## NP_004439.to.1layhid11     -1.843682132
## NP_005226.to.1layhid11     -0.922951652
## NP_004388.to.1layhid11      1.223779823
## NP_001229372.to.1layhid11   1.505024636
## NP_005130.to.1layhid11      1.868501234
## NP_004243.to.1layhid11      0.354239391
## NP_003144.to.1layhid11      0.904762058
## NP_001171551.to.1layhid11  -0.810885489
## NP_072096.to.1layhid11      0.196931698
## NP_940869.to.1layhid11     -0.763672904
## NP_005484.to.1layhid11     -0.185101226
## NP_056513.to.1layhid11     -1.234713956
## NP_061170.to.1layhid11      1.415066569
## NP_653304.to.1layhid11     -0.299649159
## NP_653081.to.1layhid11     -0.068580817
## NP_057164.to.1layhid11     -0.511326994
## NP_006627.to.1layhid11      1.194669052
## NP_004453.to.1layhid11     -0.987525862
## NP_071739.to.1layhid11      0.051437804
## NP_060337.to.1layhid11     -1.749575526
## NP_001186744.to.1layhid11  -0.334557742
## NP_001186745.to.1layhid11   0.545199896
## NP_001257810.to.1layhid11  -1.260278547
## NP_003212.to.1layhid11      0.338795627
## NP_060866.to.1layhid11     -1.061722810
## NP_001160163.to.1layhid11  -1.383219015
## NP_004499.to.1layhid11      2.574178227
## NP_006345.to.1layhid11     -0.032929835
## NP_003875.to.1layhid11     -0.338926263
## NP_002677.to.1layhid11      3.117943734
## NP_579917.to.1layhid11     -0.154079145
## NP_001135891.to.1layhid11  -0.286194458
## NP_004522.to.1layhid11     -1.209547210
## NP_003767.to.1layhid11     -1.756710111
## NP_848597.to.1layhid11      0.154421750
## NP_005970.to.1layhid11      0.632374378
## NP_060182.to.1layhid11     -0.631777053
## NP_001035492.to.1layhid11   1.008182091
## NP_899229.to.1layhid11     -0.311236788
## NP_660344.to.1layhid11      0.750227936
## Intercept.to.1layhid12     -0.935092644
## NP_579899.to.1layhid12     -0.504065583
## NP_038479.to.1layhid12     -0.546571242
## NP_001258898.to.1layhid12   0.392943242
## NP_542785.to.1layhid12      2.697782692
## NP_065821.to.1layhid12     -0.524885137
## NP_055644.to.1layhid12     -0.541847542
## NP_001371.to.1layhid12     -0.928554477
## NP_002005.to.1layhid12     -0.364074213
## XP_003846537.to.1layhid12   0.237465741
## NP_660208.to.1layhid12     -0.323530138
## NP_004439.to.1layhid12     -2.074504146
## NP_005226.to.1layhid12      0.669768878
## NP_004388.to.1layhid12      0.772344166
## NP_001229372.to.1layhid12  -0.781060765
## NP_005130.to.1layhid12      0.367882239
## NP_004243.to.1layhid12      1.613306250
## NP_003144.to.1layhid12      0.736209443
## NP_001171551.to.1layhid12   0.464702657
## NP_072096.to.1layhid12      3.131464790
## NP_940869.to.1layhid12      1.543311064
## NP_005484.to.1layhid12     -0.277605522
## NP_056513.to.1layhid12      1.374483142
## NP_061170.to.1layhid12     -0.292876214
## NP_653304.to.1layhid12     -0.454360150
## NP_653081.to.1layhid12     -0.172710585
## NP_057164.to.1layhid12     -0.548710494
## NP_006627.to.1layhid12     -0.470579652
## NP_004453.to.1layhid12     -0.056172475
## NP_071739.to.1layhid12     -1.016413678
## NP_060337.to.1layhid12     -0.992689237
## NP_001186744.to.1layhid12   0.116538403
## NP_001186745.to.1layhid12  -0.730908140
## NP_001257810.to.1layhid12   0.819102739
## NP_003212.to.1layhid12     -0.470725282
## NP_060866.to.1layhid12     -2.130401195
## NP_001160163.to.1layhid12   0.851068957
## NP_004499.to.1layhid12     -0.260650075
## NP_006345.to.1layhid12     -0.349654805
## NP_003875.to.1layhid12      0.505287599
## NP_002677.to.1layhid12     -1.059074250
## NP_579917.to.1layhid12     -0.167668284
## NP_001135891.to.1layhid12  -0.907945856
## NP_004522.to.1layhid12      1.229408913
## NP_003767.to.1layhid12      0.829132132
## NP_848597.to.1layhid12      0.143366843
## NP_005970.to.1layhid12     -0.111971626
## NP_060182.to.1layhid12      2.286109430
## NP_001035492.to.1layhid12   1.256383886
## NP_899229.to.1layhid12      1.102420255
## NP_660344.to.1layhid12     -0.934721031
## Intercept.to.1layhid13     -0.391299643
## NP_579899.to.1layhid13      0.007103594
## NP_038479.to.1layhid13      0.947854385
## NP_001258898.to.1layhid13   1.227043410
## NP_542785.to.1layhid13     -0.462677550
## NP_065821.to.1layhid13      1.291903214
## NP_055644.to.1layhid13     -0.017399495
## NP_001371.to.1layhid13      1.124590583
## NP_002005.to.1layhid13      0.721141317
## XP_003846537.to.1layhid13  -1.287014191
## NP_660208.to.1layhid13      0.588984415
## NP_004439.to.1layhid13      0.270338640
## NP_005226.to.1layhid13      0.974263589
## NP_004388.to.1layhid13     -0.172208195
## NP_001229372.to.1layhid13   0.333735493
## NP_005130.to.1layhid13      0.037685844
## NP_004243.to.1layhid13      0.972450823
## NP_003144.to.1layhid13     -0.362911914
## NP_001171551.to.1layhid13   0.465355149
## NP_072096.to.1layhid13      0.744334764
## NP_940869.to.1layhid13      0.488698155
## NP_005484.to.1layhid13     -1.908133054
## NP_056513.to.1layhid13      0.601901180
## NP_061170.to.1layhid13      1.116167676
## NP_653304.to.1layhid13      0.543204938
## NP_653081.to.1layhid13      0.821041767
## NP_057164.to.1layhid13     -2.365850282
## NP_006627.to.1layhid13      1.701486656
## NP_004453.to.1layhid13     -0.700689754
## NP_071739.to.1layhid13      1.626318713
## NP_060337.to.1layhid13      1.839074909
## NP_001186744.to.1layhid13   1.242237284
## NP_001186745.to.1layhid13  -0.787388225
## NP_001257810.to.1layhid13   1.337719067
## NP_003212.to.1layhid13      1.622720090
## NP_060866.to.1layhid13      1.677502760
## NP_001160163.to.1layhid13   0.340101457
## NP_004499.to.1layhid13      0.424323775
## NP_006345.to.1layhid13     -0.771463163
## NP_003875.to.1layhid13     -1.517566048
## NP_002677.to.1layhid13     -1.069754287
## NP_579917.to.1layhid13     -1.232467476
## NP_001135891.to.1layhid13  -0.665037455
## NP_004522.to.1layhid13      0.023770661
## NP_003767.to.1layhid13      1.287705553
## NP_848597.to.1layhid13     -0.343535462
## NP_005970.to.1layhid13     -0.251651727
## NP_060182.to.1layhid13      0.425152965
## NP_001035492.to.1layhid13  -1.153378040
## NP_899229.to.1layhid13     -0.435090841
## NP_660344.to.1layhid13      0.629401535
## Intercept.to.1layhid14      0.324187072
## NP_579899.to.1layhid14     -0.477850795
## NP_038479.to.1layhid14     -1.572499354
## NP_001258898.to.1layhid14   2.843924301
## NP_542785.to.1layhid14     -0.169153026
## NP_065821.to.1layhid14      1.126183711
## NP_055644.to.1layhid14      1.464155979
## NP_001371.to.1layhid14     -0.347430679
## NP_002005.to.1layhid14     -1.025810910
## XP_003846537.to.1layhid14  -0.729312548
## NP_660208.to.1layhid14     -0.527781405
## NP_004439.to.1layhid14      0.163674441
## NP_005226.to.1layhid14     -1.543571607
## NP_004388.to.1layhid14      1.418351461
## NP_001229372.to.1layhid14   0.551062628
## NP_005130.to.1layhid14     -0.801684157
## NP_004243.to.1layhid14     -3.107248934
## NP_003144.to.1layhid14     -1.564281641
## NP_001171551.to.1layhid14  -1.738447978
## NP_072096.to.1layhid14     -1.517531473
## NP_940869.to.1layhid14     -0.236930249
## NP_005484.to.1layhid14      0.447571623
## NP_056513.to.1layhid14     -1.111389545
## NP_061170.to.1layhid14     -2.372778210
## NP_653304.to.1layhid14      0.001225292
## NP_653081.to.1layhid14      0.242409299
## NP_057164.to.1layhid14     -1.655675453
## NP_006627.to.1layhid14      1.012287959
## NP_004453.to.1layhid14      0.967064350
## NP_071739.to.1layhid14     -1.402334471
## NP_060337.to.1layhid14      0.272908015
## NP_001186744.to.1layhid14  -0.010006275
## NP_001186745.to.1layhid14  -0.933633066
## NP_001257810.to.1layhid14  -2.513725797
## NP_003212.to.1layhid14     -0.279962276
## NP_060866.to.1layhid14     -0.343133579
## NP_001160163.to.1layhid14  -0.520363091
## NP_004499.to.1layhid14     -0.921722586
## NP_006345.to.1layhid14      0.440522563
## NP_003875.to.1layhid14     -0.366643088
## NP_002677.to.1layhid14      0.763079605
## NP_579917.to.1layhid14     -0.597194317
## NP_001135891.to.1layhid14  -0.171056575
## NP_004522.to.1layhid14      1.375869724
## NP_003767.to.1layhid14     -0.862364889
## NP_848597.to.1layhid14      0.083581369
## NP_005970.to.1layhid14     -0.719217413
## NP_060182.to.1layhid14      0.569571374
## NP_001035492.to.1layhid14   0.331910276
## NP_899229.to.1layhid14     -0.345027842
## NP_660344.to.1layhid14      0.603526516
## Intercept.to.1layhid15      0.716980402
## NP_579899.to.1layhid15      0.839668160
## NP_038479.to.1layhid15     -1.113265256
## NP_001258898.to.1layhid15   0.240068019
## NP_542785.to.1layhid15     -1.567066328
## NP_065821.to.1layhid15     -0.845208822
## NP_055644.to.1layhid15     -1.996581057
## NP_001371.to.1layhid15      1.060371307
## NP_002005.to.1layhid15      1.720168794
## XP_003846537.to.1layhid15   1.810614428
## NP_660208.to.1layhid15     -1.260113846
## NP_004439.to.1layhid15     -0.919408832
## NP_005226.to.1layhid15      1.604590814
## NP_004388.to.1layhid15      0.940908200
## NP_001229372.to.1layhid15  -1.101239369
## NP_005130.to.1layhid15     -0.210170011
## NP_004243.to.1layhid15     -0.392311420
## NP_003144.to.1layhid15     -1.059268934
## NP_001171551.to.1layhid15   0.762751160
## NP_072096.to.1layhid15      0.312393840
## NP_940869.to.1layhid15     -0.687344384
## NP_005484.to.1layhid15     -1.474568840
## NP_056513.to.1layhid15     -0.897990261
## NP_061170.to.1layhid15     -1.252120777
## NP_653304.to.1layhid15      0.670113904
## NP_653081.to.1layhid15     -2.919641291
## NP_057164.to.1layhid15     -1.409601009
## NP_006627.to.1layhid15     -1.497447271
## NP_004453.to.1layhid15     -3.017060446
## NP_071739.to.1layhid15      0.177179866
## NP_060337.to.1layhid15     -1.621582474
## NP_001186744.to.1layhid15   0.145829158
## NP_001186745.to.1layhid15  -0.543972158
## NP_001257810.to.1layhid15   1.685217079
## NP_003212.to.1layhid15      1.831591611
## NP_060866.to.1layhid15     -2.553272224
## NP_001160163.to.1layhid15  -1.306105967
## NP_004499.to.1layhid15      0.784880418
## NP_006345.to.1layhid15      1.019515188
## NP_003875.to.1layhid15      0.465984151
## NP_002677.to.1layhid15      0.383729723
## NP_579917.to.1layhid15      0.514388214
## NP_001135891.to.1layhid15   1.411461844
## NP_004522.to.1layhid15     -0.329190349
## NP_003767.to.1layhid15     -0.124572729
## NP_848597.to.1layhid15      0.572419593
## NP_005970.to.1layhid15      0.127960072
## NP_060182.to.1layhid15      1.079268900
## NP_001035492.to.1layhid15   0.086111882
## NP_899229.to.1layhid15     -1.425465151
## NP_660344.to.1layhid15     -0.256043357
## Intercept.to.1layhid16      1.862515410
## NP_579899.to.1layhid16     -0.954894218
## NP_038479.to.1layhid16     -0.555479865
## NP_001258898.to.1layhid16  -0.347962174
## NP_542785.to.1layhid16     -0.555328893
## NP_065821.to.1layhid16      0.810763421
## NP_055644.to.1layhid16      0.822801079
## NP_001371.to.1layhid16     -0.988793830
## NP_002005.to.1layhid16      0.095084842
## XP_003846537.to.1layhid16   0.855301006
## NP_660208.to.1layhid16      0.643667537
## NP_004439.to.1layhid16      0.142744900
## NP_005226.to.1layhid16      0.268425418
## NP_004388.to.1layhid16      0.132598183
## NP_001229372.to.1layhid16   0.531000430
## NP_005130.to.1layhid16     -0.139969581
## NP_004243.to.1layhid16     -0.161436389
## NP_003144.to.1layhid16     -0.432885397
## NP_001171551.to.1layhid16  -0.895862953
## NP_072096.to.1layhid16      0.658639870
## NP_940869.to.1layhid16     -1.844200816
## NP_005484.to.1layhid16      0.209373625
## NP_056513.to.1layhid16     -0.694467009
## NP_061170.to.1layhid16      0.460932113
## NP_653304.to.1layhid16     -0.666147463
## NP_653081.to.1layhid16     -0.684546391
## NP_057164.to.1layhid16      3.152124687
## NP_006627.to.1layhid16     -0.073460963
## NP_004453.to.1layhid16     -0.609083229
## NP_071739.to.1layhid16      1.819897781
## NP_060337.to.1layhid16      1.265230535
## NP_001186744.to.1layhid16  -1.525306329
## NP_001186745.to.1layhid16   0.958575488
## NP_001257810.to.1layhid16   1.322047332
## NP_003212.to.1layhid16      0.272039600
## NP_060866.to.1layhid16      4.488563543
## NP_001160163.to.1layhid16   0.144015794
## NP_004499.to.1layhid16     -2.244513674
## NP_006345.to.1layhid16      0.163247124
## NP_003875.to.1layhid16      0.753517556
## NP_002677.to.1layhid16      1.166239111
## NP_579917.to.1layhid16      0.156052568
## NP_001135891.to.1layhid16   0.602645578
## NP_004522.to.1layhid16      1.716079020
## NP_003767.to.1layhid16      0.851760697
## NP_848597.to.1layhid16      0.705646950
## NP_005970.to.1layhid16     -1.427498637
## NP_060182.to.1layhid16     -0.281690729
## NP_001035492.to.1layhid16   0.593733119
## NP_899229.to.1layhid16     -1.069542753
## NP_660344.to.1layhid16      0.505599578
## Intercept.to.1layhid17     -0.461612110
## NP_579899.to.1layhid17     -0.066225633
## NP_038479.to.1layhid17      0.157938801
## NP_001258898.to.1layhid17  -0.240103839
## NP_542785.to.1layhid17      1.546107190
## NP_065821.to.1layhid17      0.784513097
## NP_055644.to.1layhid17     -1.188368021
## NP_001371.to.1layhid17     -0.666015127
## NP_002005.to.1layhid17     -0.256092816
## XP_003846537.to.1layhid17   1.036708090
## NP_660208.to.1layhid17     -0.948835923
## NP_004439.to.1layhid17      0.797267427
## NP_005226.to.1layhid17      0.416586727
## NP_004388.to.1layhid17      1.209533710
## NP_001229372.to.1layhid17  -0.151942024
## NP_005130.to.1layhid17      0.896013525
## NP_004243.to.1layhid17      0.615640104
## NP_003144.to.1layhid17      0.152038148
## NP_001171551.to.1layhid17   0.225097765
## NP_072096.to.1layhid17     -1.425073125
## NP_940869.to.1layhid17      0.085631310
## NP_005484.to.1layhid17      0.285913801
## NP_056513.to.1layhid17      0.655690361
## NP_061170.to.1layhid17     -1.283633341
## NP_653304.to.1layhid17      1.115709706
## NP_653081.to.1layhid17      0.187241500
## NP_057164.to.1layhid17     -0.001447482
## NP_006627.to.1layhid17      1.415564256
## NP_004453.to.1layhid17      1.247835949
## NP_071739.to.1layhid17      0.742851602
## NP_060337.to.1layhid17     -0.862091893
## NP_001186744.to.1layhid17  -0.598315780
## NP_001186745.to.1layhid17   0.478988635
## NP_001257810.to.1layhid17  -0.006478226
## NP_003212.to.1layhid17      0.115826784
## NP_060866.to.1layhid17     -0.298029343
## NP_001160163.to.1layhid17  -0.504447335
## NP_004499.to.1layhid17     -0.124788684
## NP_006345.to.1layhid17      0.048966888
## NP_003875.to.1layhid17     -1.015724265
## NP_002677.to.1layhid17     -0.235435908
## NP_579917.to.1layhid17     -0.846569861
## NP_001135891.to.1layhid17   0.700018247
## NP_004522.to.1layhid17     -1.145701380
## NP_003767.to.1layhid17      0.694508818
## NP_848597.to.1layhid17      1.142587192
## NP_005970.to.1layhid17     -1.935967886
## NP_060182.to.1layhid17      0.193273229
## NP_001035492.to.1layhid17   0.136522048
## NP_899229.to.1layhid17      0.274138335
## NP_660344.to.1layhid17      1.409890642
## Intercept.to.1layhid18      0.933406032
## NP_579899.to.1layhid18     -0.146858179
## NP_038479.to.1layhid18      0.830357718
## NP_001258898.to.1layhid18   0.040434846
## NP_542785.to.1layhid18      0.206376697
## NP_065821.to.1layhid18      1.456271057
## NP_055644.to.1layhid18     -0.274364656
## NP_001371.to.1layhid18      0.379708311
## NP_002005.to.1layhid18     -1.509976080
## XP_003846537.to.1layhid18  -0.943477677
## NP_660208.to.1layhid18     -0.756872692
## NP_004439.to.1layhid18     -0.220402110
## NP_005226.to.1layhid18     -0.311518854
## NP_004388.to.1layhid18     -0.093489700
## NP_001229372.to.1layhid18  -0.602472596
## NP_005130.to.1layhid18      0.278707064
## NP_004243.to.1layhid18      0.266606831
## NP_003144.to.1layhid18      0.822430766
## NP_001171551.to.1layhid18  -1.210036424
## NP_072096.to.1layhid18      0.825347989
## NP_940869.to.1layhid18      0.513418287
## NP_005484.to.1layhid18     -0.116158116
## NP_056513.to.1layhid18     -1.922173205
## NP_061170.to.1layhid18      1.480874934
## NP_653304.to.1layhid18     -0.339804797
## NP_653081.to.1layhid18      0.960961904
## NP_057164.to.1layhid18      0.477989701
## NP_006627.to.1layhid18      0.221590516
## NP_004453.to.1layhid18     -0.599619269
## NP_071739.to.1layhid18      0.226118555
## NP_060337.to.1layhid18     -0.808829248
## NP_001186744.to.1layhid18   0.778444180
## NP_001186745.to.1layhid18  -0.679758942
## NP_001257810.to.1layhid18  -0.151329121
## NP_003212.to.1layhid18     -1.277161988
## NP_060866.to.1layhid18     -0.223828803
## NP_001160163.to.1layhid18  -0.177530232
## NP_004499.to.1layhid18     -0.565365961
## NP_006345.to.1layhid18     -0.207476145
## NP_003875.to.1layhid18     -0.054995880
## NP_002677.to.1layhid18     -0.182534380
## NP_579917.to.1layhid18     -1.116600496
## NP_001135891.to.1layhid18   0.748116772
## NP_004522.to.1layhid18     -1.294190637
## NP_003767.to.1layhid18      1.713675235
## NP_848597.to.1layhid18      0.405276317
## NP_005970.to.1layhid18      0.034952797
## NP_060182.to.1layhid18     -0.445763758
## NP_001035492.to.1layhid18   1.619899869
## NP_899229.to.1layhid18      0.507684369
## NP_660344.to.1layhid18      0.366317964
## Intercept.to.1layhid19     -1.944228087
## NP_579899.to.1layhid19      1.801293719
## NP_038479.to.1layhid19      2.542513170
## NP_001258898.to.1layhid19   0.230948725
## NP_542785.to.1layhid19      0.202439827
## NP_065821.to.1layhid19     -1.581902453
## NP_055644.to.1layhid19     -0.412542561
## NP_001371.to.1layhid19     -0.728916274
## NP_002005.to.1layhid19      0.249042986
## XP_003846537.to.1layhid19  -0.915960396
## NP_660208.to.1layhid19      0.605339320
## NP_004439.to.1layhid19     -0.006714390
## NP_005226.to.1layhid19     -0.728322527
## NP_004388.to.1layhid19     -0.040821785
## NP_001229372.to.1layhid19  -0.669326207
## NP_005130.to.1layhid19     -2.076236076
## NP_004243.to.1layhid19      0.403590251
## NP_003144.to.1layhid19      0.557201769
## NP_001171551.to.1layhid19   1.669515802
## NP_072096.to.1layhid19      1.363025080
## NP_940869.to.1layhid19     -0.361791479
## NP_005484.to.1layhid19     -0.156414913
## NP_056513.to.1layhid19     -0.224882566
## NP_061170.to.1layhid19     -1.107212113
## NP_653304.to.1layhid19     -0.184213693
## NP_653081.to.1layhid19     -1.740617335
## NP_057164.to.1layhid19     -0.751155184
## NP_006627.to.1layhid19     -0.541912139
## NP_004453.to.1layhid19      0.737756471
## NP_071739.to.1layhid19      0.281075308
## NP_060337.to.1layhid19     -0.693144316
## NP_001186744.to.1layhid19  -0.310548114
## NP_001186745.to.1layhid19  -0.094155785
## NP_001257810.to.1layhid19  -1.299696105
## NP_003212.to.1layhid19      0.067977095
## NP_060866.to.1layhid19     -0.594701220
## NP_001160163.to.1layhid19   0.119122555
## NP_004499.to.1layhid19     -0.039410601
## NP_006345.to.1layhid19      1.233881750
## NP_003875.to.1layhid19      1.332894176
## NP_002677.to.1layhid19      0.931368344
## NP_579917.to.1layhid19     -0.551951754
## NP_001135891.to.1layhid19   1.713654774
## NP_004522.to.1layhid19     -0.070968418
## NP_003767.to.1layhid19      1.189401373
## NP_848597.to.1layhid19      1.419059626
## NP_005970.to.1layhid19     -0.793839475
## NP_060182.to.1layhid19      1.218213878
## NP_001035492.to.1layhid19   0.448902369
## NP_899229.to.1layhid19     -0.824860997
## NP_660344.to.1layhid19      1.693069270
## Intercept.to.1layhid20     -0.585005148
## NP_579899.to.1layhid20     -1.150670509
## NP_038479.to.1layhid20     -1.840918372
## NP_001258898.to.1layhid20  -0.030980554
## NP_542785.to.1layhid20      0.991858171
## NP_065821.to.1layhid20     -0.163141173
## NP_055644.to.1layhid20     -0.531580964
## NP_001371.to.1layhid20      1.385936245
## NP_002005.to.1layhid20     -0.600440349
## XP_003846537.to.1layhid20   1.393591392
## NP_660208.to.1layhid20     -1.205392407
## NP_004439.to.1layhid20      0.033384762
## NP_005226.to.1layhid20      0.098340282
## NP_004388.to.1layhid20     -1.116770397
## NP_001229372.to.1layhid20   0.090122129
## NP_005130.to.1layhid20      2.651473507
## NP_004243.to.1layhid20      0.755117407
## NP_003144.to.1layhid20     -1.547412631
## NP_001171551.to.1layhid20   0.377795187
## NP_072096.to.1layhid20     -0.700200819
## NP_940869.to.1layhid20     -0.550512869
## NP_005484.to.1layhid20     -0.964520841
## NP_056513.to.1layhid20      0.131209709
## NP_061170.to.1layhid20      0.636091903
## NP_653304.to.1layhid20      0.335149299
## NP_653081.to.1layhid20     -0.070784173
## NP_057164.to.1layhid20      0.224608111
## NP_006627.to.1layhid20      0.745297109
## NP_004453.to.1layhid20     -0.785403409
## NP_071739.to.1layhid20      1.725680323
## NP_060337.to.1layhid20      0.835396564
## NP_001186744.to.1layhid20   1.520800483
## NP_001186745.to.1layhid20   0.989196453
## NP_001257810.to.1layhid20   0.527161531
## NP_003212.to.1layhid20     -1.379648008
## NP_060866.to.1layhid20      1.453141115
## NP_001160163.to.1layhid20   1.741838554
## NP_004499.to.1layhid20     -1.010571156
## NP_006345.to.1layhid20     -2.616790506
## NP_003875.to.1layhid20      0.224300778
## NP_002677.to.1layhid20      1.104972091
## NP_579917.to.1layhid20     -0.300997208
## NP_001135891.to.1layhid20  -0.533218453
## NP_004522.to.1layhid20      0.517324288
## NP_003767.to.1layhid20      0.791929966
## NP_848597.to.1layhid20      0.115444320
## NP_005970.to.1layhid20     -1.310936460
## NP_060182.to.1layhid20     -0.222151460
## NP_001035492.to.1layhid20  -0.056161067
## NP_899229.to.1layhid20     -0.030186599
## NP_660344.to.1layhid20     -1.935608838
## Intercept.to.1layhid21      0.153465644
## NP_579899.to.1layhid21     -0.784832218
## NP_038479.to.1layhid21      0.441074928
## NP_001258898.to.1layhid21   0.178507735
## NP_542785.to.1layhid21      1.568191750
## NP_065821.to.1layhid21      0.980922680
## NP_055644.to.1layhid21      0.658669806
## NP_001371.to.1layhid21     -1.924074045
## NP_002005.to.1layhid21     -1.970100176
## XP_003846537.to.1layhid21   0.358022832
## NP_660208.to.1layhid21      1.706032712
## NP_004439.to.1layhid21     -0.608240130
## NP_005226.to.1layhid21     -1.757491602
## NP_004388.to.1layhid21      0.513283021
## NP_001229372.to.1layhid21   1.551158795
## NP_005130.to.1layhid21     -0.420181254
## NP_004243.to.1layhid21      1.824523363
## NP_003144.to.1layhid21     -0.230797869
## NP_001171551.to.1layhid21  -0.100099344
## NP_072096.to.1layhid21     -0.474299344
## NP_940869.to.1layhid21     -1.739828041
## NP_005484.to.1layhid21     -3.289345240
## NP_056513.to.1layhid21     -0.131283308
## NP_061170.to.1layhid21     -0.789700287
## NP_653304.to.1layhid21     -0.082284981
## NP_653081.to.1layhid21     -1.994805072
## NP_057164.to.1layhid21     -0.320431425
## NP_006627.to.1layhid21      0.399497941
## NP_004453.to.1layhid21     -0.258908047
## NP_071739.to.1layhid21     -0.709273457
## NP_060337.to.1layhid21      0.765114642
## NP_001186744.to.1layhid21  -2.746137442
## NP_001186745.to.1layhid21  -2.061064907
## NP_001257810.to.1layhid21   1.514671606
## NP_003212.to.1layhid21      2.121780041
## NP_060866.to.1layhid21     -0.153924338
## NP_001160163.to.1layhid21  -0.675913130
## NP_004499.to.1layhid21      0.141435458
## NP_006345.to.1layhid21      1.180267265
## NP_003875.to.1layhid21      1.917108351
## NP_002677.to.1layhid21     -1.254798381
## NP_579917.to.1layhid21     -0.650889062
## NP_001135891.to.1layhid21  -1.602947024
## NP_004522.to.1layhid21     -1.928799329
## NP_003767.to.1layhid21      1.487815657
## NP_848597.to.1layhid21     -0.287871093
## NP_005970.to.1layhid21      0.958806423
## NP_060182.to.1layhid21      0.453871279
## NP_001035492.to.1layhid21  -0.460534056
## NP_899229.to.1layhid21      1.278740758
## NP_660344.to.1layhid21      1.027791582
## Intercept.to.1layhid22     -1.460431092
## NP_579899.to.1layhid22     -1.908880927
## NP_038479.to.1layhid22     -1.419726530
## NP_001258898.to.1layhid22  -0.331746644
## NP_542785.to.1layhid22      0.523456319
## NP_065821.to.1layhid22     -0.283462059
## NP_055644.to.1layhid22      0.058821147
## NP_001371.to.1layhid22     -1.244278011
## NP_002005.to.1layhid22      0.878111826
## XP_003846537.to.1layhid22  -0.948810203
## NP_660208.to.1layhid22      1.475406277
## NP_004439.to.1layhid22      0.313042957
## NP_005226.to.1layhid22      0.467037111
## NP_004388.to.1layhid22     -0.310726771
## NP_001229372.to.1layhid22  -1.278906107
## NP_005130.to.1layhid22     -2.842879215
## NP_004243.to.1layhid22      0.553591497
## NP_003144.to.1layhid22     -0.799527377
## NP_001171551.to.1layhid22  -0.380644478
## NP_072096.to.1layhid22      0.048856898
## NP_940869.to.1layhid22      0.425541477
## NP_005484.to.1layhid22     -1.522147175
## NP_056513.to.1layhid22     -0.440616250
## NP_061170.to.1layhid22     -1.900151528
## NP_653304.to.1layhid22     -1.420040401
## NP_653081.to.1layhid22      0.094790306
## NP_057164.to.1layhid22     -0.818779078
## NP_006627.to.1layhid22      0.844094247
## NP_004453.to.1layhid22     -0.337373263
## NP_071739.to.1layhid22      2.284147677
## NP_060337.to.1layhid22      0.668564206
## NP_001186744.to.1layhid22  -0.195265911
## NP_001186745.to.1layhid22  -0.197792115
## NP_001257810.to.1layhid22  -1.893391391
## NP_003212.to.1layhid22      1.212851111
## NP_060866.to.1layhid22      2.375328791
## NP_001160163.to.1layhid22   0.868706488
## NP_004499.to.1layhid22      2.629965154
## NP_006345.to.1layhid22     -0.615519573
## NP_003875.to.1layhid22     -0.570612750
## NP_002677.to.1layhid22      1.727894382
## NP_579917.to.1layhid22      0.721065752
## NP_001135891.to.1layhid22   1.240000871
## NP_004522.to.1layhid22      0.591545159
## NP_003767.to.1layhid22      2.134089250
## NP_848597.to.1layhid22     -1.036806175
## NP_005970.to.1layhid22     -0.683633510
## NP_060182.to.1layhid22      0.654211166
## NP_001035492.to.1layhid22  -1.249351744
## NP_899229.to.1layhid22     -0.098710573
## NP_660344.to.1layhid22     -3.288401507
## Intercept.to.1layhid23      0.612485105
## NP_579899.to.1layhid23     -1.988673910
## NP_038479.to.1layhid23     -0.628758508
## NP_001258898.to.1layhid23  -1.148075496
## NP_542785.to.1layhid23      2.271411775
## NP_065821.to.1layhid23      0.584482759
## NP_055644.to.1layhid23      0.360222583
## NP_001371.to.1layhid23      0.704462199
## NP_002005.to.1layhid23      0.687917696
## XP_003846537.to.1layhid23  -0.188820107
## NP_660208.to.1layhid23      1.070293739
## NP_004439.to.1layhid23     -0.239392901
## NP_005226.to.1layhid23     -1.906273633
## NP_004388.to.1layhid23      1.039054316
## NP_001229372.to.1layhid23   0.159804718
## NP_005130.to.1layhid23      0.414039166
## NP_004243.to.1layhid23      0.894863246
## NP_003144.to.1layhid23     -0.797778410
## NP_001171551.to.1layhid23   0.043044082
## NP_072096.to.1layhid23      1.943249693
## NP_940869.to.1layhid23     -0.704379092
## NP_005484.to.1layhid23      1.481219398
## NP_056513.to.1layhid23     -0.554840165
## NP_061170.to.1layhid23      1.945237103
## NP_653304.to.1layhid23     -0.522191348
## NP_653081.to.1layhid23      0.235536176
## NP_057164.to.1layhid23     -0.629076844
## NP_006627.to.1layhid23      1.537822313
## NP_004453.to.1layhid23      0.270627275
## NP_071739.to.1layhid23      1.036854410
## NP_060337.to.1layhid23      2.463890817
## NP_001186744.to.1layhid23  -0.737031116
## NP_001186745.to.1layhid23   0.433351157
## NP_001257810.to.1layhid23   0.613653835
## NP_003212.to.1layhid23     -1.605317574
## NP_060866.to.1layhid23      1.039573613
## NP_001160163.to.1layhid23   1.774953796
## NP_004499.to.1layhid23      2.508728540
## NP_006345.to.1layhid23      0.005177406
## NP_003875.to.1layhid23     -0.110684032
## NP_002677.to.1layhid23     -0.580957316
## NP_579917.to.1layhid23      1.955262624
## NP_001135891.to.1layhid23  -0.137973994
## NP_004522.to.1layhid23      1.271503084
## NP_003767.to.1layhid23     -1.874796592
## NP_848597.to.1layhid23     -1.874237689
## NP_005970.to.1layhid23     -1.704034086
## NP_060182.to.1layhid23      2.315739447
## NP_001035492.to.1layhid23  -0.601793868
## NP_899229.to.1layhid23     -2.792440241
## NP_660344.to.1layhid23     -0.376651427
## Intercept.to.1layhid24     -1.871084447
## NP_579899.to.1layhid24      1.346976072
## NP_038479.to.1layhid24      0.333364218
## NP_001258898.to.1layhid24   0.050658913
## NP_542785.to.1layhid24     -1.998720328
## NP_065821.to.1layhid24      1.075952798
## NP_055644.to.1layhid24     -0.524047452
## NP_001371.to.1layhid24      0.594541181
## NP_002005.to.1layhid24     -0.170213725
## XP_003846537.to.1layhid24   0.422328620
## NP_660208.to.1layhid24      1.131187795
## NP_004439.to.1layhid24     -1.381939008
## NP_005226.to.1layhid24     -1.708227102
## NP_004388.to.1layhid24      0.816514548
## NP_001229372.to.1layhid24  -1.404471056
## NP_005130.to.1layhid24     -0.520371117
## NP_004243.to.1layhid24      0.205507249
## NP_003144.to.1layhid24     -0.303005239
## NP_001171551.to.1layhid24   3.249395758
## NP_072096.to.1layhid24      0.089100530
## NP_940869.to.1layhid24      0.458891852
## NP_005484.to.1layhid24     -0.158558024
## NP_056513.to.1layhid24     -0.268662351
## NP_061170.to.1layhid24      0.800953644
## NP_653304.to.1layhid24     -1.277245305
## NP_653081.to.1layhid24     -0.011909938
## NP_057164.to.1layhid24     -0.324187664
## NP_006627.to.1layhid24      1.603969787
## NP_004453.to.1layhid24     -0.748465471
## NP_071739.to.1layhid24     -0.441006468
## NP_060337.to.1layhid24      1.750560531
## NP_001186744.to.1layhid24   0.517224309
## NP_001186745.to.1layhid24  -0.106426849
## NP_001257810.to.1layhid24   0.475076119
## NP_003212.to.1layhid24      2.107803985
## NP_060866.to.1layhid24      1.627655797
## NP_001160163.to.1layhid24  -2.051981927
## NP_004499.to.1layhid24      0.410324783
## NP_006345.to.1layhid24      1.236045402
## NP_003875.to.1layhid24      0.265901270
## NP_002677.to.1layhid24      0.463357474
## NP_579917.to.1layhid24      1.526674811
## NP_001135891.to.1layhid24   1.398908637
## NP_004522.to.1layhid24      1.558908464
## NP_003767.to.1layhid24     -0.444453826
## NP_848597.to.1layhid24     -0.409845813
## NP_005970.to.1layhid24      0.426160477
## NP_060182.to.1layhid24     -0.090491806
## NP_001035492.to.1layhid24   0.776436511
## NP_899229.to.1layhid24     -3.092135812
## NP_660344.to.1layhid24      1.533787344
## Intercept.to.1layhid25      1.444096344
## NP_579899.to.1layhid25      0.547123419
## NP_038479.to.1layhid25      0.937388778
## NP_001258898.to.1layhid25  -1.657739303
## NP_542785.to.1layhid25      1.620684323
## NP_065821.to.1layhid25     -1.625183619
## NP_055644.to.1layhid25     -0.330272021
## NP_001371.to.1layhid25      0.675241993
## NP_002005.to.1layhid25     -1.213827936
## XP_003846537.to.1layhid25   0.210514742
## NP_660208.to.1layhid25      0.601853693
## NP_004439.to.1layhid25     -0.176456283
## NP_005226.to.1layhid25      0.595468187
## NP_004388.to.1layhid25      0.644521459
## NP_001229372.to.1layhid25  -0.592668219
## NP_005130.to.1layhid25      0.358232676
## NP_004243.to.1layhid25      1.180730419
## NP_003144.to.1layhid25      0.402746924
## NP_001171551.to.1layhid25   0.498788834
## NP_072096.to.1layhid25     -0.037824163
## NP_940869.to.1layhid25      0.194218899
## NP_005484.to.1layhid25      0.466005164
## NP_056513.to.1layhid25     -1.249622145
## NP_061170.to.1layhid25     -0.995732111
## NP_653304.to.1layhid25      0.864014243
## NP_653081.to.1layhid25     -2.082465499
## NP_057164.to.1layhid25      2.547642749
## NP_006627.to.1layhid25     -0.617077337
## NP_004453.to.1layhid25     -0.180196964
## NP_071739.to.1layhid25     -1.346575129
## NP_060337.to.1layhid25     -1.144100338
## NP_001186744.to.1layhid25  -2.959024010
## NP_001186745.to.1layhid25  -2.103739540
## NP_001257810.to.1layhid25   1.116737252
## NP_003212.to.1layhid25     -0.715181678
## NP_060866.to.1layhid25     -0.301386086
## NP_001160163.to.1layhid25  -0.782026049
## NP_004499.to.1layhid25     -0.374443369
## NP_006345.to.1layhid25      0.892454680
## NP_003875.to.1layhid25     -0.472189580
## NP_002677.to.1layhid25     -0.176130552
## NP_579917.to.1layhid25      0.567102694
## NP_001135891.to.1layhid25  -0.295702826
## NP_004522.to.1layhid25     -0.914420589
## NP_003767.to.1layhid25     -0.476139496
## NP_848597.to.1layhid25     -0.975996096
## NP_005970.to.1layhid25     -0.949358667
## NP_060182.to.1layhid25      1.079120948
## NP_001035492.to.1layhid25   2.376210470
## NP_899229.to.1layhid25     -1.159357691
## NP_660344.to.1layhid25      1.682742759
## Intercept.to.1layhid26      0.045213416
## NP_579899.to.1layhid26      0.960296762
## NP_038479.to.1layhid26      1.373872578
## NP_001258898.to.1layhid26  -1.540291104
## NP_542785.to.1layhid26      0.760811537
## NP_065821.to.1layhid26      1.543662403
## NP_055644.to.1layhid26      0.095098898
## NP_001371.to.1layhid26     -0.525614469
## NP_002005.to.1layhid26     -1.244004897
## XP_003846537.to.1layhid26   1.745198799
## NP_660208.to.1layhid26      0.498804766
## NP_004439.to.1layhid26     -1.404392278
## NP_005226.to.1layhid26     -0.404796771
## NP_004388.to.1layhid26     -2.084874318
## NP_001229372.to.1layhid26   0.686412584
## NP_005130.to.1layhid26      0.635137708
## NP_004243.to.1layhid26      0.184752218
## NP_003144.to.1layhid26      0.608046941
## NP_001171551.to.1layhid26   0.114057277
## NP_072096.to.1layhid26      0.434413241
## NP_940869.to.1layhid26     -0.288971350
## NP_005484.to.1layhid26      1.635307379
## NP_056513.to.1layhid26     -0.011898375
## NP_061170.to.1layhid26      1.550362136
## NP_653304.to.1layhid26     -3.042018921
## NP_653081.to.1layhid26     -0.120479403
## NP_057164.to.1layhid26      1.305955983
## NP_006627.to.1layhid26     -0.998822711
## NP_004453.to.1layhid26     -0.561862464
## NP_071739.to.1layhid26     -2.207225368
## NP_060337.to.1layhid26     -0.380928992
## NP_001186744.to.1layhid26   0.682181589
## NP_001186745.to.1layhid26  -2.837828945
## NP_001257810.to.1layhid26  -1.394626983
## NP_003212.to.1layhid26     -0.682315100
## NP_060866.to.1layhid26     -0.815857035
## NP_001160163.to.1layhid26  -2.198609366
## NP_004499.to.1layhid26     -1.355975111
## NP_006345.to.1layhid26     -0.009474467
## NP_003875.to.1layhid26     -1.418484680
## NP_002677.to.1layhid26     -1.019061857
## NP_579917.to.1layhid26      0.793269265
## NP_001135891.to.1layhid26  -0.493694985
## NP_004522.to.1layhid26     -1.391438151
## NP_003767.to.1layhid26     -1.177993337
## NP_848597.to.1layhid26     -0.396075847
## NP_005970.to.1layhid26      0.202146638
## NP_060182.to.1layhid26     -0.893600192
## NP_001035492.to.1layhid26   1.035703988
## NP_899229.to.1layhid26     -0.553749593
## NP_660344.to.1layhid26      2.448913089
## Intercept.to.1layhid27      0.612605989
## NP_579899.to.1layhid27     -0.619772642
## NP_038479.to.1layhid27     -2.814489301
## NP_001258898.to.1layhid27  -1.231053848
## NP_542785.to.1layhid27      2.426989658
## NP_065821.to.1layhid27     -2.465105810
## NP_055644.to.1layhid27      0.936000271
## NP_001371.to.1layhid27      0.011839426
## NP_002005.to.1layhid27     -0.324936286
## XP_003846537.to.1layhid27   0.227450622
## NP_660208.to.1layhid27     -0.764212695
## NP_004439.to.1layhid27     -1.168497392
## NP_005226.to.1layhid27     -0.460118304
## NP_004388.to.1layhid27     -2.598179123
## NP_001229372.to.1layhid27   0.195325317
## NP_005130.to.1layhid27     -1.494279428
## NP_004243.to.1layhid27      0.493461552
## NP_003144.to.1layhid27      0.023162998
## NP_001171551.to.1layhid27  -0.117035003
## NP_072096.to.1layhid27      2.004639963
## NP_940869.to.1layhid27      2.142928658
## NP_005484.to.1layhid27      0.522224095
## NP_056513.to.1layhid27      1.746914186
## NP_061170.to.1layhid27      0.345529712
## NP_653304.to.1layhid27     -0.727466650
## NP_653081.to.1layhid27     -1.654473957
## NP_057164.to.1layhid27     -1.499222807
## NP_006627.to.1layhid27     -0.828569943
## NP_004453.to.1layhid27      0.349005988
## NP_071739.to.1layhid27     -1.642340604
## NP_060337.to.1layhid27     -0.545711730
## NP_001186744.to.1layhid27  -1.293448496
## NP_001186745.to.1layhid27   0.389327933
## NP_001257810.to.1layhid27  -0.037476823
## NP_003212.to.1layhid27      1.256026863
## NP_060866.to.1layhid27      0.332241241
## NP_001160163.to.1layhid27  -0.411748628
## NP_004499.to.1layhid27      0.148684420
## NP_006345.to.1layhid27      1.312182102
## NP_003875.to.1layhid27     -0.771457983
## NP_002677.to.1layhid27      0.202127009
## NP_579917.to.1layhid27      0.286523758
## NP_001135891.to.1layhid27  -0.374687854
## NP_004522.to.1layhid27      0.307285678
## NP_003767.to.1layhid27      0.365837664
## NP_848597.to.1layhid27      0.459387662
## NP_005970.to.1layhid27     -0.947488293
## NP_060182.to.1layhid27     -0.173486737
## NP_001035492.to.1layhid27   2.282501768
## NP_899229.to.1layhid27      0.203222632
## NP_660344.to.1layhid27     -1.405195397
## Intercept.to.1layhid28     -0.166220010
## NP_579899.to.1layhid28      1.669515398
## NP_038479.to.1layhid28     -0.168867316
## NP_001258898.to.1layhid28  -0.994900817
## NP_542785.to.1layhid28      0.556321439
## NP_065821.to.1layhid28      1.421331706
## NP_055644.to.1layhid28     -0.291707570
## NP_001371.to.1layhid28      0.620794852
## NP_002005.to.1layhid28      1.619804658
## XP_003846537.to.1layhid28  -0.074900088
## NP_660208.to.1layhid28      0.979489696
## NP_004439.to.1layhid28      1.692255083
## NP_005226.to.1layhid28      0.659964505
## NP_004388.to.1layhid28      0.727837552
## NP_001229372.to.1layhid28   0.227760867
## NP_005130.to.1layhid28     -1.317281388
## NP_004243.to.1layhid28     -1.545646385
## NP_003144.to.1layhid28     -1.346180092
## NP_001171551.to.1layhid28  -1.468991904
## NP_072096.to.1layhid28      1.031811015
## NP_940869.to.1layhid28      0.211305052
## NP_005484.to.1layhid28      0.082882907
## NP_056513.to.1layhid28      1.314405270
## NP_061170.to.1layhid28     -0.621768608
## NP_653304.to.1layhid28     -0.748144150
## NP_653081.to.1layhid28     -1.660362105
## NP_057164.to.1layhid28      2.093503111
## NP_006627.to.1layhid28     -1.327613468
## NP_004453.to.1layhid28      0.235693581
## NP_071739.to.1layhid28      0.151994605
## NP_060337.to.1layhid28      3.412930939
## NP_001186744.to.1layhid28  -0.856421692
## NP_001186745.to.1layhid28   1.183707296
## NP_001257810.to.1layhid28   1.660300909
## NP_003212.to.1layhid28     -0.273784950
## NP_060866.to.1layhid28      1.776934651
## NP_001160163.to.1layhid28  -0.223037959
## NP_004499.to.1layhid28      0.655725390
## NP_006345.to.1layhid28      0.435165246
## NP_003875.to.1layhid28      1.963985951
## NP_002677.to.1layhid28     -0.572079830
## NP_579917.to.1layhid28     -0.875466548
## NP_001135891.to.1layhid28   1.729496018
## NP_004522.to.1layhid28     -0.161773569
## NP_003767.to.1layhid28     -0.323180457
## NP_848597.to.1layhid28      0.903473707
## NP_005970.to.1layhid28      0.895477389
## NP_060182.to.1layhid28     -1.447835445
## NP_001035492.to.1layhid28   2.161726416
## NP_899229.to.1layhid28      0.584516265
## NP_660344.to.1layhid28     -0.253268697
## Intercept.to.1layhid29      1.219568659
## NP_579899.to.1layhid29      0.599817857
## NP_038479.to.1layhid29     -1.610709290
## NP_001258898.to.1layhid29  -0.362339489
## NP_542785.to.1layhid29      0.968483769
## NP_065821.to.1layhid29     -0.172852596
## NP_055644.to.1layhid29     -0.074721943
## NP_001371.to.1layhid29     -2.002456067
## NP_002005.to.1layhid29     -0.592387390
## XP_003846537.to.1layhid29  -0.927404361
## NP_660208.to.1layhid29      1.407124061
## NP_004439.to.1layhid29     -1.037255626
## NP_005226.to.1layhid29     -0.108718714
## NP_004388.to.1layhid29     -0.230340603
## NP_001229372.to.1layhid29   0.686456788
## NP_005130.to.1layhid29     -0.630247157
## NP_004243.to.1layhid29     -0.443988645
## NP_003144.to.1layhid29      0.699344921
## NP_001171551.to.1layhid29  -0.802940459
## NP_072096.to.1layhid29     -0.774188391
## NP_940869.to.1layhid29      0.130825753
## NP_005484.to.1layhid29      0.202688580
## NP_056513.to.1layhid29     -0.171092013
## NP_061170.to.1layhid29      2.784509579
## NP_653304.to.1layhid29     -0.670751605
## NP_653081.to.1layhid29      1.791284180
## NP_057164.to.1layhid29     -1.350271369
## NP_006627.to.1layhid29     -1.018611566
## NP_004453.to.1layhid29      0.027140243
## NP_071739.to.1layhid29     -2.046896108
## NP_060337.to.1layhid29     -1.445804231
## NP_001186744.to.1layhid29  -0.796779341
## NP_001186745.to.1layhid29  -0.802413398
## NP_001257810.to.1layhid29   0.692731557
## NP_003212.to.1layhid29      1.028105166
## NP_060866.to.1layhid29      1.725930162
## NP_001160163.to.1layhid29   1.729987862
## NP_004499.to.1layhid29      0.926432053
## NP_006345.to.1layhid29     -0.765822939
## NP_003875.to.1layhid29      0.554413628
## NP_002677.to.1layhid29      1.134712680
## NP_579917.to.1layhid29      0.649683105
## NP_001135891.to.1layhid29   0.503201451
## NP_004522.to.1layhid29     -0.410519139
## NP_003767.to.1layhid29      0.290254575
## NP_848597.to.1layhid29      0.099426115
## NP_005970.to.1layhid29     -0.858915640
## NP_060182.to.1layhid29     -1.083306254
## NP_001035492.to.1layhid29   0.654758297
## NP_899229.to.1layhid29      0.792067698
## NP_660344.to.1layhid29     -0.472082791
## Intercept.to.1layhid30      1.237098967
## NP_579899.to.1layhid30     -0.157423150
## NP_038479.to.1layhid30     -1.154314439
## NP_001258898.to.1layhid30   0.377895642
## NP_542785.to.1layhid30      0.922719566
## NP_065821.to.1layhid30      0.927829255
## NP_055644.to.1layhid30      0.496911973
## NP_001371.to.1layhid30      1.632702210
## NP_002005.to.1layhid30      0.312517729
## XP_003846537.to.1layhid30  -0.394418554
## NP_660208.to.1layhid30     -0.566459234
## NP_004439.to.1layhid30      1.695976075
## NP_005226.to.1layhid30      0.260933081
## NP_004388.to.1layhid30     -1.341158766
## NP_001229372.to.1layhid30  -0.865025416
## NP_005130.to.1layhid30      2.171809288
## NP_004243.to.1layhid30      1.874102363
## NP_003144.to.1layhid30     -1.489372493
## NP_001171551.to.1layhid30  -1.949974418
## NP_072096.to.1layhid30     -2.734452945
## NP_940869.to.1layhid30     -0.205804279
## NP_005484.to.1layhid30     -0.534239394
## NP_056513.to.1layhid30      0.978758267
## NP_061170.to.1layhid30     -0.072521029
## NP_653304.to.1layhid30      0.262402891
## NP_653081.to.1layhid30      1.458242091
## NP_057164.to.1layhid30      1.342061313
## NP_006627.to.1layhid30     -1.102818615
## NP_004453.to.1layhid30      0.222801806
## NP_071739.to.1layhid30      0.361528760
## NP_060337.to.1layhid30     -0.524969877
## NP_001186744.to.1layhid30   1.367927356
## NP_001186745.to.1layhid30   1.441386075
## NP_001257810.to.1layhid30   2.443447098
## NP_003212.to.1layhid30      0.924529536
## NP_060866.to.1layhid30      0.240588295
## NP_001160163.to.1layhid30   0.810679153
## NP_004499.to.1layhid30      0.651999980
## NP_006345.to.1layhid30      0.055460698
## NP_003875.to.1layhid30      0.621711700
## NP_002677.to.1layhid30     -0.708597107
## NP_579917.to.1layhid30     -0.957237460
## NP_001135891.to.1layhid30  -0.307231742
## NP_004522.to.1layhid30      1.159165546
## NP_003767.to.1layhid30      0.254909188
## NP_848597.to.1layhid30      0.862568636
## NP_005970.to.1layhid30      0.385297853
## NP_060182.to.1layhid30     -0.225944856
## NP_001035492.to.1layhid30  -0.419520091
## NP_899229.to.1layhid30      0.321156846
## NP_660344.to.1layhid30      1.924693282
## Intercept.to.2layhid1      -0.047776793
## 1layhid1.to.2layhid1        0.383729454
## 1layhid2.to.2layhid1        0.127908062
## 1layhid3.to.2layhid1        0.584314908
## 1layhid4.to.2layhid1       -0.778197987
## 1layhid5.to.2layhid1        1.261304780
## 1layhid6.to.2layhid1       -0.680707949
## 1layhid7.to.2layhid1        1.350256073
## 1layhid8.to.2layhid1        0.903255761
## 1layhid9.to.2layhid1       -0.359645774
## 1layhid10.to.2layhid1      -1.211905688
## 1layhid11.to.2layhid1      -0.339927800
## 1layhid12.to.2layhid1       2.177696981
## 1layhid13.to.2layhid1       0.877646697
## 1layhid14.to.2layhid1      -1.713293322
## 1layhid15.to.2layhid1       1.829539025
## 1layhid16.to.2layhid1       2.405802022
## 1layhid17.to.2layhid1       0.835753165
## 1layhid18.to.2layhid1       0.462435943
## 1layhid19.to.2layhid1      -0.174483134
## 1layhid20.to.2layhid1      -0.047619164
## 1layhid21.to.2layhid1       0.697111994
## 1layhid22.to.2layhid1       0.412975371
## 1layhid23.to.2layhid1      -1.222325753
## 1layhid24.to.2layhid1      -1.419409018
## 1layhid25.to.2layhid1       2.946707014
## 1layhid26.to.2layhid1       0.656479264
## 1layhid27.to.2layhid1       1.061540076
## 1layhid28.to.2layhid1      -1.026989982
## 1layhid29.to.2layhid1      -0.569550513
## 1layhid30.to.2layhid1      -0.697190390
## Intercept.to.2layhid2       0.435648165
## 1layhid1.to.2layhid2       -0.192643052
## 1layhid2.to.2layhid2        0.174306657
## 1layhid3.to.2layhid2        1.083209480
## 1layhid4.to.2layhid2       -3.044521048
## 1layhid5.to.2layhid2       -2.399927164
## 1layhid6.to.2layhid2       -0.573246588
## 1layhid7.to.2layhid2       -0.618585903
## 1layhid8.to.2layhid2        0.037288182
## 1layhid9.to.2layhid2       -1.055786156
## 1layhid10.to.2layhid2       1.281156818
## 1layhid11.to.2layhid2       0.583612707
## 1layhid12.to.2layhid2      -0.401653867
## 1layhid13.to.2layhid2       0.944231588
## 1layhid14.to.2layhid2       1.297385894
## 1layhid15.to.2layhid2      -2.748015286
## 1layhid16.to.2layhid2      -0.160815185
## 1layhid17.to.2layhid2       1.795666277
## 1layhid18.to.2layhid2      -0.578990349
## 1layhid19.to.2layhid2      -0.102792071
## 1layhid20.to.2layhid2      -1.193511353
## 1layhid21.to.2layhid2      -0.349861288
## 1layhid22.to.2layhid2      -0.299939027
## 1layhid23.to.2layhid2       0.446943964
## 1layhid24.to.2layhid2      -1.470676217
## 1layhid25.to.2layhid2       1.590033648
## 1layhid26.to.2layhid2      -0.234813341
## 1layhid27.to.2layhid2       0.909917670
## 1layhid28.to.2layhid2       0.807692301
## 1layhid29.to.2layhid2      -0.467453068
## 1layhid30.to.2layhid2      -1.020936468
## Intercept.to.2layhid3      -1.392604625
## 1layhid1.to.2layhid3        1.492024200
## 1layhid2.to.2layhid3       -0.492681401
## 1layhid3.to.2layhid3        0.855816589
## 1layhid4.to.2layhid3       -2.459328642
## 1layhid5.to.2layhid3        0.803011662
## 1layhid6.to.2layhid3       -0.434081477
## 1layhid7.to.2layhid3       -1.705989558
## 1layhid8.to.2layhid3        3.727863679
## 1layhid9.to.2layhid3        0.117661621
## 1layhid10.to.2layhid3      -0.382878167
## 1layhid11.to.2layhid3      -0.296492878
## 1layhid12.to.2layhid3      -0.807351356
## 1layhid13.to.2layhid3      -0.303711236
## 1layhid14.to.2layhid3      -0.292832511
## 1layhid15.to.2layhid3       0.190187171
## 1layhid16.to.2layhid3       0.992962984
## 1layhid17.to.2layhid3      -1.774384932
## 1layhid18.to.2layhid3       1.884829622
## 1layhid19.to.2layhid3      -1.353048339
## 1layhid20.to.2layhid3       4.192436329
## 1layhid21.to.2layhid3      -0.418033329
## 1layhid22.to.2layhid3       1.859301391
## 1layhid23.to.2layhid3       1.275193479
## 1layhid24.to.2layhid3       0.092633902
## 1layhid25.to.2layhid3      -0.281998742
## 1layhid26.to.2layhid3      -1.574058815
## 1layhid27.to.2layhid3      -0.143721729
## 1layhid28.to.2layhid3       0.131105764
## 1layhid29.to.2layhid3       0.365528630
## 1layhid30.to.2layhid3      -1.195878904
## Intercept.to.2layhid4      -0.794088306
## 1layhid1.to.2layhid4        1.236761354
## 1layhid2.to.2layhid4       -0.872347144
## 1layhid3.to.2layhid4        0.458208319
## 1layhid4.to.2layhid4       -1.939501022
## 1layhid5.to.2layhid4       -0.529687389
## 1layhid6.to.2layhid4        2.460296079
## 1layhid7.to.2layhid4        2.325656104
## 1layhid8.to.2layhid4        0.285292219
## 1layhid9.to.2layhid4       -1.660818216
## 1layhid10.to.2layhid4       0.198468405
## 1layhid11.to.2layhid4      -2.169057791
## 1layhid12.to.2layhid4       0.218257198
## 1layhid13.to.2layhid4      -0.194225087
## 1layhid14.to.2layhid4       0.669240765
## 1layhid15.to.2layhid4       0.230246534
## 1layhid16.to.2layhid4       0.040557471
## 1layhid17.to.2layhid4      -1.302732139
## 1layhid18.to.2layhid4       0.755752282
## 1layhid19.to.2layhid4       0.060235958
## 1layhid20.to.2layhid4       0.990884736
## 1layhid21.to.2layhid4      -0.196782688
## 1layhid22.to.2layhid4      -0.183142597
## 1layhid23.to.2layhid4       0.516704103
## 1layhid24.to.2layhid4      -0.327718624
## 1layhid25.to.2layhid4       0.340990022
## 1layhid26.to.2layhid4       0.333775860
## 1layhid27.to.2layhid4      -1.387469292
## 1layhid28.to.2layhid4      -0.050671912
## 1layhid29.to.2layhid4      -0.849599475
## 1layhid30.to.2layhid4      -0.128909267
## Intercept.to.2layhid5       1.086544971
## 1layhid1.to.2layhid5        2.634041192
## 1layhid2.to.2layhid5        0.389898419
## 1layhid3.to.2layhid5       -1.728733070
## 1layhid4.to.2layhid5       -2.802353442
## 1layhid5.to.2layhid5        1.302431051
## 1layhid6.to.2layhid5        1.236712340
## 1layhid7.to.2layhid5       -0.034902020
## 1layhid8.to.2layhid5        0.870313011
## 1layhid9.to.2layhid5        0.331239771
## 1layhid10.to.2layhid5      -0.695140191
## 1layhid11.to.2layhid5       0.064979899
## 1layhid12.to.2layhid5      -0.264859339
## 1layhid13.to.2layhid5       1.273152222
## 1layhid14.to.2layhid5      -0.059097155
## 1layhid15.to.2layhid5       0.152043296
## 1layhid16.to.2layhid5      -1.338746934
## 1layhid17.to.2layhid5       1.619871047
## 1layhid18.to.2layhid5       1.077968057
## 1layhid19.to.2layhid5      -0.293114430
## 1layhid20.to.2layhid5       0.442270061
## 1layhid21.to.2layhid5      -1.581903390
## 1layhid22.to.2layhid5       1.173726043
## 1layhid23.to.2layhid5       0.908836180
## 1layhid24.to.2layhid5      -1.659189954
## 1layhid25.to.2layhid5      -1.407602618
## 1layhid26.to.2layhid5      -1.944352108
## 1layhid27.to.2layhid5      -0.324671750
## 1layhid28.to.2layhid5      -1.761157201
## 1layhid29.to.2layhid5       2.469158508
## 1layhid30.to.2layhid5       0.935625116
## Intercept.to.2layhid6       0.211019853
## 1layhid1.to.2layhid6       -0.288002410
## 1layhid2.to.2layhid6       -0.631833268
## 1layhid3.to.2layhid6        0.819855534
## 1layhid4.to.2layhid6       -1.800129645
## 1layhid5.to.2layhid6       -1.456294517
## 1layhid6.to.2layhid6       -1.110413704
## 1layhid7.to.2layhid6       -1.626832438
## 1layhid8.to.2layhid6       -0.433571565
## 1layhid9.to.2layhid6       -0.006434052
## 1layhid10.to.2layhid6       1.793740208
## 1layhid11.to.2layhid6      -0.491073436
## 1layhid12.to.2layhid6       0.522791098
## 1layhid13.to.2layhid6      -0.382727285
## 1layhid14.to.2layhid6      -0.428501490
## 1layhid15.to.2layhid6       0.229796911
## 1layhid16.to.2layhid6       0.295534518
## 1layhid17.to.2layhid6       0.358606849
## 1layhid18.to.2layhid6       0.435629390
## 1layhid19.to.2layhid6       0.778864723
## 1layhid20.to.2layhid6      -0.708190385
## 1layhid21.to.2layhid6       0.063600914
## 1layhid22.to.2layhid6      -2.289255837
## 1layhid23.to.2layhid6      -1.805796302
## 1layhid24.to.2layhid6       0.318665861
## 1layhid25.to.2layhid6       0.991153601
## 1layhid26.to.2layhid6       1.443765437
## 1layhid27.to.2layhid6      -0.344564966
## 1layhid28.to.2layhid6       1.371820463
## 1layhid29.to.2layhid6      -2.270188814
## 1layhid30.to.2layhid6      -0.334045192
## Intercept.to.2layhid7      -0.953007855
## 1layhid1.to.2layhid7        0.360500579
## 1layhid2.to.2layhid7       -0.431643045
## 1layhid3.to.2layhid7        1.614561582
## 1layhid4.to.2layhid7        0.280926472
## 1layhid5.to.2layhid7        0.479111525
## 1layhid6.to.2layhid7       -1.350329559
## 1layhid7.to.2layhid7       -0.163351029
## 1layhid8.to.2layhid7        0.042359720
## 1layhid9.to.2layhid7       -0.804825456
## 1layhid10.to.2layhid7      -0.412091151
## 1layhid11.to.2layhid7       0.526939829
## 1layhid12.to.2layhid7       0.612523293
## 1layhid13.to.2layhid7      -0.777711082
## 1layhid14.to.2layhid7      -0.206713836
## 1layhid15.to.2layhid7       0.218073121
## 1layhid16.to.2layhid7      -0.813409447
## 1layhid17.to.2layhid7       0.122170174
## 1layhid18.to.2layhid7       2.316360221
## 1layhid19.to.2layhid7      -1.351883987
## 1layhid20.to.2layhid7       0.358881658
## 1layhid21.to.2layhid7       0.496649017
## 1layhid22.to.2layhid7      -1.916300458
## 1layhid23.to.2layhid7      -1.103827152
## 1layhid24.to.2layhid7      -0.860834594
## 1layhid25.to.2layhid7       0.612460000
## 1layhid26.to.2layhid7       0.157541048
## 1layhid27.to.2layhid7      -0.421596720
## 1layhid28.to.2layhid7       0.394888803
## 1layhid29.to.2layhid7      -1.747585416
## 1layhid30.to.2layhid7      -0.063053423
## Intercept.to.2layhid8      -0.155985484
## 1layhid1.to.2layhid8        0.580296182
## 1layhid2.to.2layhid8       -1.186840896
## 1layhid3.to.2layhid8        0.178392117
## 1layhid4.to.2layhid8       -2.818507395
## 1layhid5.to.2layhid8       -3.053635698
## 1layhid6.to.2layhid8       -2.502735033
## 1layhid7.to.2layhid8       -3.760854134
## 1layhid8.to.2layhid8        1.738206404
## 1layhid9.to.2layhid8       -0.043971902
## 1layhid10.to.2layhid8       1.071853967
## 1layhid11.to.2layhid8       0.960737000
## 1layhid12.to.2layhid8      -0.815531497
## 1layhid13.to.2layhid8      -2.170792224
## 1layhid14.to.2layhid8       1.648122161
## 1layhid15.to.2layhid8      -0.699333327
## 1layhid16.to.2layhid8      -0.830379074
## 1layhid17.to.2layhid8      -0.349896122
## 1layhid18.to.2layhid8       1.081960556
## 1layhid19.to.2layhid8      -2.666449661
## 1layhid20.to.2layhid8      -0.683321453
## 1layhid21.to.2layhid8      -0.938419154
## 1layhid22.to.2layhid8      -0.460246135
## 1layhid23.to.2layhid8       0.932532017
## 1layhid24.to.2layhid8      -2.540338657
## 1layhid25.to.2layhid8       2.069156601
## 1layhid26.to.2layhid8      -0.013236115
## 1layhid27.to.2layhid8       1.605998792
## 1layhid28.to.2layhid8      -0.378417310
## 1layhid29.to.2layhid8      -0.019349909
## 1layhid30.to.2layhid8      -0.187389297
## Intercept.to.2layhid9      -0.053861352
## 1layhid1.to.2layhid9       -1.483904132
## 1layhid2.to.2layhid9       -1.878528798
## 1layhid3.to.2layhid9        0.505239488
## 1layhid4.to.2layhid9       -1.498287001
## 1layhid5.to.2layhid9       -0.413872322
## 1layhid6.to.2layhid9       -1.830652404
## 1layhid7.to.2layhid9       -1.915903628
## 1layhid8.to.2layhid9        0.912152220
## 1layhid9.to.2layhid9       -1.174343833
## 1layhid10.to.2layhid9       0.751901146
## 1layhid11.to.2layhid9       1.472161444
## 1layhid12.to.2layhid9       0.621874819
## 1layhid13.to.2layhid9       0.588578999
## 1layhid14.to.2layhid9       2.868813295
## 1layhid15.to.2layhid9      -1.064022659
## 1layhid16.to.2layhid9      -3.815007942
## 1layhid17.to.2layhid9       1.316263556
## 1layhid18.to.2layhid9      -0.241188435
## 1layhid19.to.2layhid9      -0.223566662
## 1layhid20.to.2layhid9      -0.556679378
## 1layhid21.to.2layhid9       1.079023643
## 1layhid22.to.2layhid9       0.326510969
## 1layhid23.to.2layhid9      -0.412458514
## 1layhid24.to.2layhid9      -1.018987757
## 1layhid25.to.2layhid9      -0.077044060
## 1layhid26.to.2layhid9       0.476860400
## 1layhid27.to.2layhid9       0.380580532
## 1layhid28.to.2layhid9      -0.352699036
## 1layhid29.to.2layhid9       1.476804992
## 1layhid30.to.2layhid9       1.793658818
## Intercept.to.2layhid10     -0.011277509
## 1layhid1.to.2layhid10       1.250957460
## 1layhid2.to.2layhid10       0.114906590
## 1layhid3.to.2layhid10      -0.533387244
## 1layhid4.to.2layhid10       0.721062002
## 1layhid5.to.2layhid10       1.369458415
## 1layhid6.to.2layhid10      -1.408470593
## 1layhid7.to.2layhid10       0.663302957
## 1layhid8.to.2layhid10       0.477347405
## 1layhid9.to.2layhid10      -0.131385147
## 1layhid10.to.2layhid10     -2.062495979
## 1layhid11.to.2layhid10      2.085150494
## 1layhid12.to.2layhid10     -0.577987992
## 1layhid13.to.2layhid10      1.450624039
## 1layhid14.to.2layhid10     -0.757757175
## 1layhid15.to.2layhid10     -0.199204926
## 1layhid16.to.2layhid10      0.827188735
## 1layhid17.to.2layhid10      0.816416766
## 1layhid18.to.2layhid10     -0.439491587
## 1layhid19.to.2layhid10      0.215877078
## 1layhid20.to.2layhid10     -1.196046480
## 1layhid21.to.2layhid10     -0.585039763
## 1layhid22.to.2layhid10      1.798664642
## 1layhid23.to.2layhid10      0.807084609
## 1layhid24.to.2layhid10      0.696366848
## 1layhid25.to.2layhid10     -2.202650095
## 1layhid26.to.2layhid10     -0.498091095
## 1layhid27.to.2layhid10      0.807966217
## 1layhid28.to.2layhid10      0.634341727
## 1layhid29.to.2layhid10     -0.086489819
## 1layhid30.to.2layhid10      1.263459524
## Intercept.to.2layhid11      0.356946304
## 1layhid1.to.2layhid11      -1.275165936
## 1layhid2.to.2layhid11       0.243848450
## 1layhid3.to.2layhid11       0.581525799
## 1layhid4.to.2layhid11      -1.101141856
## 1layhid5.to.2layhid11       0.014389266
## 1layhid6.to.2layhid11      -1.527912078
## 1layhid7.to.2layhid11      -0.925279982
## 1layhid8.to.2layhid11      -0.621659140
## 1layhid9.to.2layhid11      -1.106965291
## 1layhid10.to.2layhid11      2.603108762
## 1layhid11.to.2layhid11     -0.677268038
## 1layhid12.to.2layhid11      0.547940556
## 1layhid13.to.2layhid11     -3.841175547
## 1layhid14.to.2layhid11      1.582408692
## 1layhid15.to.2layhid11      0.378166832
## 1layhid16.to.2layhid11     -0.644874430
## 1layhid17.to.2layhid11      0.430549291
## 1layhid18.to.2layhid11     -0.230375701
## 1layhid19.to.2layhid11      1.136438090
## 1layhid20.to.2layhid11      0.512058253
## 1layhid21.to.2layhid11      0.433759314
## 1layhid22.to.2layhid11     -2.555371409
## 1layhid23.to.2layhid11      0.181296857
## 1layhid24.to.2layhid11      0.619348414
## 1layhid25.to.2layhid11      2.216624768
## 1layhid26.to.2layhid11      0.585246128
## 1layhid27.to.2layhid11     -0.372788885
## 1layhid28.to.2layhid11      1.390718940
## 1layhid29.to.2layhid11     -0.613907640
## 1layhid30.to.2layhid11      0.139977028
## Intercept.to.2layhid12      0.071509787
## 1layhid1.to.2layhid12      -1.072118509
## 1layhid2.to.2layhid12       0.666077123
## 1layhid3.to.2layhid12       2.139938922
## 1layhid4.to.2layhid12      -0.468536406
## 1layhid5.to.2layhid12       1.111859419
## 1layhid6.to.2layhid12       3.507318163
## 1layhid7.to.2layhid12       0.517010748
## 1layhid8.to.2layhid12       0.585960267
## 1layhid9.to.2layhid12      -1.118099165
## 1layhid10.to.2layhid12     -0.275541406
## 1layhid11.to.2layhid12     -0.288717253
## 1layhid12.to.2layhid12      0.767341525
## 1layhid13.to.2layhid12     -2.410208780
## 1layhid14.to.2layhid12     -0.415018531
## 1layhid15.to.2layhid12     -0.518994082
## 1layhid16.to.2layhid12      3.113228101
## 1layhid17.to.2layhid12     -0.434970331
## 1layhid18.to.2layhid12     -0.349209081
## 1layhid19.to.2layhid12     -0.610925703
## 1layhid20.to.2layhid12      1.117155675
## 1layhid21.to.2layhid12      0.350084799
## 1layhid22.to.2layhid12      0.701114020
## 1layhid23.to.2layhid12      2.878493046
## 1layhid24.to.2layhid12     -0.474198097
## 1layhid25.to.2layhid12      2.512613911
## 1layhid26.to.2layhid12      0.441168989
## 1layhid27.to.2layhid12      1.116810864
## 1layhid28.to.2layhid12     -0.130211262
## 1layhid29.to.2layhid12     -3.238575743
## 1layhid30.to.2layhid12     -1.357339741
## Intercept.to.2layhid13      1.301535081
## 1layhid1.to.2layhid13      -0.523002017
## 1layhid2.to.2layhid13      -0.794721420
## 1layhid3.to.2layhid13       0.045909970
## 1layhid4.to.2layhid13       1.005803415
## 1layhid5.to.2layhid13      -0.048892586
## 1layhid6.to.2layhid13      -1.308703149
## 1layhid7.to.2layhid13      -1.478998624
## 1layhid8.to.2layhid13      -0.818065084
## 1layhid9.to.2layhid13       1.007200183
## 1layhid10.to.2layhid13      1.170102062
## 1layhid11.to.2layhid13     -0.735683692
## 1layhid12.to.2layhid13      0.886209854
## 1layhid13.to.2layhid13      0.003736929
## 1layhid14.to.2layhid13      0.033924551
## 1layhid15.to.2layhid13      0.755863938
## 1layhid16.to.2layhid13     -1.330508181
## 1layhid17.to.2layhid13      1.413073355
## 1layhid18.to.2layhid13     -0.602545874
## 1layhid19.to.2layhid13     -0.353676972
## 1layhid20.to.2layhid13     -0.977644239
## 1layhid21.to.2layhid13     -0.053746120
## 1layhid22.to.2layhid13     -0.931042996
## 1layhid23.to.2layhid13     -1.587618012
## 1layhid24.to.2layhid13      0.257742835
## 1layhid25.to.2layhid13      0.389163591
## 1layhid26.to.2layhid13      0.587788497
## 1layhid27.to.2layhid13     -0.495106693
## 1layhid28.to.2layhid13     -1.232376780
## 1layhid29.to.2layhid13      0.363824758
## 1layhid30.to.2layhid13      1.402785089
## Intercept.to.2layhid14      0.837963281
## 1layhid1.to.2layhid14      -2.235858709
## 1layhid2.to.2layhid14      -1.462314336
## 1layhid3.to.2layhid14      -1.432488983
## 1layhid4.to.2layhid14       0.846099814
## 1layhid5.to.2layhid14      -1.317096123
## 1layhid6.to.2layhid14      -0.161034038
## 1layhid7.to.2layhid14      -0.321940082
## 1layhid8.to.2layhid14      -0.668645074
## 1layhid9.to.2layhid14      -0.717099463
## 1layhid10.to.2layhid14      0.640002687
## 1layhid11.to.2layhid14      0.220404014
## 1layhid12.to.2layhid14      0.174509837
## 1layhid13.to.2layhid14      1.081818843
## 1layhid14.to.2layhid14      1.213409859
## 1layhid15.to.2layhid14      0.507044756
## 1layhid16.to.2layhid14     -2.603709807
## 1layhid17.to.2layhid14      2.696012540
## 1layhid18.to.2layhid14     -1.017317363
## 1layhid19.to.2layhid14      0.487974742
## 1layhid20.to.2layhid14      0.331499937
## 1layhid21.to.2layhid14     -1.297221548
## 1layhid22.to.2layhid14     -0.271076370
## 1layhid23.to.2layhid14     -0.335587123
## 1layhid24.to.2layhid14     -1.962025599
## 1layhid25.to.2layhid14      0.057344148
## 1layhid26.to.2layhid14     -1.088454557
## 1layhid27.to.2layhid14      0.289435253
## 1layhid28.to.2layhid14      0.386935538
## 1layhid29.to.2layhid14      1.769100898
## 1layhid30.to.2layhid14      0.044167047
## Intercept.to.2layhid15      1.436908446
## 1layhid1.to.2layhid15      -2.638745677
## 1layhid2.to.2layhid15       2.368599141
## 1layhid3.to.2layhid15       0.232049800
## 1layhid4.to.2layhid15       1.771728204
## 1layhid5.to.2layhid15       1.647089990
## 1layhid6.to.2layhid15       0.127181648
## 1layhid7.to.2layhid15      -0.293213364
## 1layhid8.to.2layhid15      -1.493187537
## 1layhid9.to.2layhid15       1.416470388
## 1layhid10.to.2layhid15     -0.146091990
## 1layhid11.to.2layhid15     -0.044550791
## 1layhid12.to.2layhid15      1.307962858
## 1layhid13.to.2layhid15     -0.162357240
## 1layhid14.to.2layhid15      0.359549343
## 1layhid15.to.2layhid15      0.714439415
## 1layhid16.to.2layhid15      0.835543760
## 1layhid17.to.2layhid15     -0.464607718
## 1layhid18.to.2layhid15      0.533397775
## 1layhid19.to.2layhid15      0.351190061
## 1layhid20.to.2layhid15      0.307483161
## 1layhid21.to.2layhid15     -0.009683989
## 1layhid22.to.2layhid15      0.486608648
## 1layhid23.to.2layhid15     -0.238569795
## 1layhid24.to.2layhid15      0.549935300
## 1layhid25.to.2layhid15     -1.076022781
## 1layhid26.to.2layhid15     -0.318238968
## 1layhid27.to.2layhid15     -0.461642406
## 1layhid28.to.2layhid15     -0.570951038
## 1layhid29.to.2layhid15     -0.503391321
## 1layhid30.to.2layhid15     -0.874534296
## Intercept.to.3layhid1       0.072691837
## 2layhid1.to.3layhid1        0.980351675
## 2layhid2.to.3layhid1       -0.153111514
## 2layhid3.to.3layhid1       -0.762001132
## 2layhid4.to.3layhid1        1.384322978
## 2layhid5.to.3layhid1       -1.910023074
## 2layhid6.to.3layhid1        1.182307960
## 2layhid7.to.3layhid1        0.116161773
## 2layhid8.to.3layhid1        0.611564181
## 2layhid9.to.3layhid1       -1.029758352
## 2layhid10.to.3layhid1      -0.949571324
## 2layhid11.to.3layhid1      -0.808512660
## 2layhid12.to.3layhid1       2.255040202
## 2layhid13.to.3layhid1      -0.228298702
## 2layhid14.to.3layhid1      -1.068636832
## 2layhid15.to.3layhid1       2.053126069
## Intercept.to.3layhid2       0.441010340
## 2layhid1.to.3layhid2        0.090038115
## 2layhid2.to.3layhid2       -2.122129651
## 2layhid3.to.3layhid2       -0.022333106
## 2layhid4.to.3layhid2        0.300419763
## 2layhid5.to.3layhid2       -0.390694948
## 2layhid6.to.3layhid2       -0.346603971
## 2layhid7.to.3layhid2        0.254214186
## 2layhid8.to.3layhid2       -2.915351571
## 2layhid9.to.3layhid2       -1.793366025
## 2layhid10.to.3layhid2       0.480518213
## 2layhid11.to.3layhid2       0.702449962
## 2layhid12.to.3layhid2       1.820737433
## 2layhid13.to.3layhid2      -2.827999972
## 2layhid14.to.3layhid2      -1.039285022
## 2layhid15.to.3layhid2       1.517879282
## Intercept.to.3layhid3      -0.687540105
## 2layhid1.to.3layhid3        1.030488132
## 2layhid2.to.3layhid3       -2.664770923
## 2layhid3.to.3layhid3       -3.148307770
## 2layhid4.to.3layhid3       -1.016966432
## 2layhid5.to.3layhid3       -2.082087297
## 2layhid6.to.3layhid3        0.335398277
## 2layhid7.to.3layhid3        1.907992651
## 2layhid8.to.3layhid3       -2.600965315
## 2layhid9.to.3layhid3        0.119615450
## 2layhid10.to.3layhid3       0.925356946
## 2layhid11.to.3layhid3       0.766742785
## 2layhid12.to.3layhid3      -1.067233244
## 2layhid13.to.3layhid3       1.751341439
## 2layhid14.to.3layhid3       0.984396083
## 2layhid15.to.3layhid3       2.253795864
## Intercept.to.3layhid4       0.288997111
## 2layhid1.to.3layhid4        1.176344514
## 2layhid2.to.3layhid4        0.636362111
## 2layhid3.to.3layhid4       -0.616509266
## 2layhid4.to.3layhid4       -0.644470729
## 2layhid5.to.3layhid4        0.612822792
## 2layhid6.to.3layhid4        0.186238445
## 2layhid7.to.3layhid4        0.800168001
## 2layhid8.to.3layhid4        1.484532774
## 2layhid9.to.3layhid4        1.189283336
## 2layhid10.to.3layhid4      -2.242938353
## 2layhid11.to.3layhid4       1.939008050
## 2layhid12.to.3layhid4      -0.901908909
## 2layhid13.to.3layhid4       1.943205988
## 2layhid14.to.3layhid4      -0.824349285
## 2layhid15.to.3layhid4       0.548078133
## Intercept.to.3layhid5      -0.347357382
## 2layhid1.to.3layhid5        0.831364476
## 2layhid2.to.3layhid5        0.708554516
## 2layhid3.to.3layhid5        0.110127288
## 2layhid4.to.3layhid5       -1.324062933
## 2layhid5.to.3layhid5        3.213376134
## 2layhid6.to.3layhid5       -0.996397275
## 2layhid7.to.3layhid5        1.176578200
## 2layhid8.to.3layhid5        0.089577078
## 2layhid9.to.3layhid5        0.212262768
## 2layhid10.to.3layhid5       2.430981034
## 2layhid11.to.3layhid5      -2.658584966
## 2layhid12.to.3layhid5      -0.345013095
## 2layhid13.to.3layhid5      -1.892821242
## 2layhid14.to.3layhid5      -0.465242551
## 2layhid15.to.3layhid5       0.517217043
## Intercept.to.3layhid6      -0.730908354
## 2layhid1.to.3layhid6       -0.814636589
## 2layhid2.to.3layhid6       -0.578796386
## 2layhid3.to.3layhid6       -0.362327058
## 2layhid4.to.3layhid6       -0.609223283
## 2layhid5.to.3layhid6        0.666069306
## 2layhid6.to.3layhid6        0.403048801
## 2layhid7.to.3layhid6       -1.032330836
## 2layhid8.to.3layhid6       -1.029929703
## 2layhid9.to.3layhid6        0.199767749
## 2layhid10.to.3layhid6      -0.381384902
## 2layhid11.to.3layhid6      -1.034937363
## 2layhid12.to.3layhid6      -1.947673623
## 2layhid13.to.3layhid6       4.237071871
## 2layhid14.to.3layhid6      -0.381465647
## 2layhid15.to.3layhid6       1.487400482
## Intercept.to.3layhid7       0.374307605
## 2layhid1.to.3layhid7       -1.302721555
## 2layhid2.to.3layhid7        1.206957649
## 2layhid3.to.3layhid7        0.669121329
## 2layhid4.to.3layhid7        0.650232934
## 2layhid5.to.3layhid7        1.116017427
## 2layhid6.to.3layhid7       -1.004649724
## 2layhid7.to.3layhid7        0.076838283
## 2layhid8.to.3layhid7        2.971777102
## 2layhid9.to.3layhid7        2.867024947
## 2layhid10.to.3layhid7      -0.625378638
## 2layhid11.to.3layhid7       1.080893673
## 2layhid12.to.3layhid7      -2.022084347
## 2layhid13.to.3layhid7      -1.226479891
## 2layhid14.to.3layhid7       1.947615495
## 2layhid15.to.3layhid7      -1.058495705
## Intercept.to.3layhid8      -0.436093974
## 2layhid1.to.3layhid8        0.028069145
## 2layhid2.to.3layhid8       -1.703349470
## 2layhid3.to.3layhid8        0.502043891
## 2layhid4.to.3layhid8       -0.453364947
## 2layhid5.to.3layhid8        1.769762995
## 2layhid6.to.3layhid8       -2.085184769
## 2layhid7.to.3layhid8       -1.027593344
## 2layhid8.to.3layhid8       -2.269647748
## 2layhid9.to.3layhid8        0.320969374
## 2layhid10.to.3layhid8       2.984868697
## 2layhid11.to.3layhid8      -1.872605561
## 2layhid12.to.3layhid8      -1.583194789
## 2layhid13.to.3layhid8       0.241134619
## 2layhid14.to.3layhid8       0.915627055
## 2layhid15.to.3layhid8       0.727319863
## Intercept.to.Basal-like     1.279755960
## 3layhid1.to.Basal-like      0.184606069
## 3layhid2.to.Basal-like     -2.545613534
## 3layhid3.to.Basal-like     -3.965390024
## 3layhid4.to.Basal-like      0.553311742
## 3layhid5.to.Basal-like     -0.703620910
## 3layhid6.to.Basal-like     -1.418908247
## 3layhid7.to.Basal-like      1.868592554
## 3layhid8.to.Basal-like     -2.919265458
## Intercept.to.HER2-enriched -1.143987912
## 3layhid1.to.HER2-enriched  -2.781977171
## 3layhid2.to.HER2-enriched  -3.827971339
## 3layhid3.to.HER2-enriched   1.250104285
## 3layhid4.to.HER2-enriched  -0.688864771
## 3layhid5.to.HER2-enriched   0.257665937
## 3layhid6.to.HER2-enriched   2.138013486
## 3layhid7.to.HER2-enriched  -0.161469750
## 3layhid8.to.HER2-enriched   2.508092309
## Intercept.to.Luminal A     -0.967177223
## 3layhid1.to.Luminal A       1.170583201
## 3layhid2.to.Luminal A       1.135225917
## 3layhid3.to.Luminal A       4.005323020
## 3layhid4.to.Luminal A      -0.938879158
## 3layhid5.to.Luminal A      -3.298513796
## 3layhid6.to.Luminal A      -0.004809811
## 3layhid7.to.Luminal A      -2.027504000
## 3layhid8.to.Luminal A      -1.884114752
## Intercept.to.Luminal B     -0.911967508
## 3layhid1.to.Luminal B      -0.728982340
## 3layhid2.to.Luminal B       2.453005662
## 3layhid3.to.Luminal B      -1.834862596
## 3layhid4.to.Luminal B      -1.968399152
## 3layhid5.to.Luminal B       1.309025590
## 3layhid6.to.Luminal B      -3.606147025
## 3layhid7.to.Luminal B      -1.511510117
## 3layhid8.to.Luminal B       3.210901834
neural.network.predicts <- compute(neural.network.mod, test_data) #prediction
neural.network.res = neural.network.predicts$net.result #results of prediction
print(neural.network.res)
##           [,1]         [,2]         [,3]        [,4]
## 6  0.036907270 0.0073295456 0.9613592279 0.005705886
## 9  0.742473970 0.0968910258 0.0008789811 0.082851551
## 10 0.719065547 0.5102246532 0.0002291823 0.235252800
## 14 0.269423692 0.0218129773 0.8097528495 0.002413882
## 19 0.763400311 0.0704935582 0.0008370741 0.205865887
## 21 0.006958227 0.9729299357 0.0050884436 0.011643144
## 22 0.006092833 0.9745151972 0.0105537397 0.005104087
## 23 0.881074040 0.0932281932 0.0036657466 0.003590610
## 37 0.007281360 0.0059784193 0.9836815960 0.003333242
## 40 0.006582216 0.0045610858 0.9831084755 0.005006926
## 43 0.015947281 0.0008929747 0.9742303382 0.058367067
## 50 0.004634111 0.0059147772 0.9796090867 0.005584340
## 51 0.002769187 0.0044226118 0.9063323465 0.186145085
## 55 0.006569920 0.0067055938 0.9838059814 0.002722012
## 59 0.005341142 0.0078544216 0.0555358678 0.981212050
## 60 0.010610334 0.0082810655 0.0164364091 0.988620930
## 64 0.011816947 0.0014800020 0.9809300875 0.021765844
## 66 0.012943049 0.0085768839 0.0142799653 0.989737529
## 72 0.006304529 0.0498144106 0.0199920123 0.768828109
## 76 0.008967837 0.0100322810 0.0170046842 0.986631664
## 78 0.042848459 0.0156493735 0.0067265696 0.974530510
neural.network.res=data.frame("neural.network.res"=ifelse(max.col(neural.network.res[ ,1:4])==1, "Basal-like",
                              ifelse(max.col(neural.network.res[ ,1:4])==2, "HER2-enriched",
                              ifelse(max.col(neural.network.res[ ,1:4])==3, "Luminal A", "Luminal B"))))
confusionMatrix(as.factor(test_data$PAM50.mRNA), as.factor(neural.network.res$neural.network.res))
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             3             0         2         0
##   HER2-enriched          1             2         0         0
##   Luminal A              0             0         6         0
##   Luminal B              0             0         1         6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.8095          
##                  95% CI : (0.5809, 0.9455)
##     No Information Rate : 0.4286          
##     P-Value [Acc > NIR] : 0.0004208       
##                                           
##                   Kappa : 0.7367          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     0.7500              1.00000           0.6667
## Specificity                     0.8824              0.94737           1.0000
## Pos Pred Value                  0.6000              0.66667           1.0000
## Neg Pred Value                  0.9375              1.00000           0.8000
## Prevalence                      0.1905              0.09524           0.4286
## Detection Rate                  0.1429              0.09524           0.2857
## Detection Prevalence            0.2381              0.14286           0.2857
## Balanced Accuracy               0.8162              0.97368           0.8333
##                      Class: Luminal B
## Sensitivity                    1.0000
## Specificity                    0.9333
## Pos Pred Value                 0.8571
## Neg Pred Value                 1.0000
## Prevalence                     0.2857
## Detection Rate                 0.2857
## Detection Prevalence           0.3333
## Balanced Accuracy              0.9667

PAM50 Data

Data modification, train and test dataset creation for PAM50

###identify PAM50 proteins
pam50 <- genes$RefSeqProteinID
pam50.ind <- which(colnames(data) %in% pam50 )
length(pam50.ind)
## [1] 38
###dividing the data set into a training data and a test data - 70% to 30%
samp <- createDataPartition(data$PAM50.mRNA, p = 0.7, list = FALSE)
train_data_pam50 <- data[samp, c(21, pam50.ind)]
summary(train_data_pam50)
##   PAM50.mRNA          NP_057427         NP_002408         NP_000415      
##  Length:59          Min.   :-2.7427   Min.   :-3.6100   Min.   :-7.4072  
##  Class :character   1st Qu.:-1.0621   1st Qu.:-1.9715   1st Qu.:-4.5258  
##  Mode  :character   Median :-0.4092   Median :-0.8404   Median :-3.3542  
##                     Mean   :-0.3310   Mean   :-0.6633   Mean   :-2.5694  
##                     3rd Qu.: 0.2617   3rd Qu.: 0.3919   3rd Qu.:-0.9787  
##                     Max.   : 2.3864   Max.   : 3.8587   Max.   : 5.6254  
##    NP_000413         NP_000517         NP_004439        NP_005219      
##  Min.   :-7.9484   Min.   :-6.3048   Min.   :-5.888   Min.   :-5.4356  
##  1st Qu.:-4.2649   1st Qu.:-3.7452   1st Qu.:-3.756   1st Qu.:-3.1943  
##  Median :-3.1184   Median :-2.4679   Median :-2.258   Median :-1.9591  
##  Mean   :-2.5716   Mean   :-1.8345   Mean   :-1.468   Mean   :-1.6950  
##  3rd Qu.:-0.6372   3rd Qu.:-0.4118   3rd Qu.:-1.027   3rd Qu.:-0.4182  
##  Max.   : 5.7383   Max.   : 5.5196   Max.   : 9.668   Max.   : 7.1587  
##    NP_058519        NP_058518       NP_001116539      NP_061155      
##  Min.   :-9.114   Min.   :-8.762   Min.   :-9.573   Min.   :-5.7241  
##  1st Qu.:-5.468   1st Qu.:-5.245   1st Qu.:-5.507   1st Qu.:-2.0541  
##  Median :-2.984   Median :-2.938   Median :-2.939   Median :-0.8508  
##  Mean   :-2.266   Mean   :-2.292   Mean   :-2.318   Mean   :-0.5507  
##  3rd Qu.: 1.409   3rd Qu.: 1.153   3rd Qu.: 1.587   3rd Qu.: 1.1712  
##  Max.   : 5.073   Max.   : 5.138   Max.   : 5.115   Max.   : 3.4804  
##   NP_001035932       NP_077006         NP_000917         NP_065178      
##  Min.   :-5.5674   Min.   :-5.5674   Min.   :-9.2227   Min.   :-2.4680  
##  1st Qu.:-1.7586   1st Qu.:-1.7572   1st Qu.:-5.5573   1st Qu.:-0.1342  
##  Median :-0.5153   Median :-0.5153   Median :-2.3640   Median : 0.5137  
##  Mean   :-0.6614   Mean   :-0.6652   Mean   :-2.1105   Mean   : 0.4605  
##  3rd Qu.: 0.5883   3rd Qu.: 0.5449   3rd Qu.: 0.4697   3rd Qu.: 1.1741  
##  Max.   : 4.0968   Max.   : 4.1044   Max.   : 5.6887   Max.   : 2.2619  
##    NP_006836         NP_006614         NP_001784         NP_006092      
##  Min.   :-2.6222   Min.   :-5.3276   Min.   :-4.5650   Min.   :-3.4802  
##  1st Qu.:-1.1826   1st Qu.:-2.1521   1st Qu.:-1.7297   1st Qu.:-1.4429  
##  Median :-0.4593   Median :-0.9030   Median :-0.3907   Median :-0.2571  
##  Mean   :-0.3229   Mean   :-0.6382   Mean   :-0.2317   Mean   :-0.2557  
##  3rd Qu.: 0.4299   3rd Qu.: 1.2996   3rd Qu.: 1.2856   3rd Qu.: 0.5431  
##  Max.   : 3.2643   Max.   : 4.3353   Max.   : 4.8474   Max.   : 3.7730  
##   NP_001153651      NP_001159403       NP_000116         NP_004314      
##  Min.   :-8.8672   Min.   :-3.7796   Min.   :-6.3326   Min.   :-3.6052  
##  1st Qu.:-4.9175   1st Qu.:-1.9218   1st Qu.:-3.7929   1st Qu.:-1.2561  
##  Median :-2.7665   Median :-0.8040   Median :-1.7839   Median :-0.4880  
##  Mean   :-1.9182   Mean   :-0.7695   Mean   :-1.3705   Mean   :-0.3145  
##  3rd Qu.: 0.5029   3rd Qu.: 0.3589   3rd Qu.: 0.8484   3rd Qu.: 0.1893  
##  Max.   : 8.4037   Max.   : 2.1838   Max.   : 4.2341   Max.   : 5.5543  
##    NP_060601         NP_005931         NP_003003         NP_113611       
##  Min.   :-7.0215   Min.   :-4.2455   Min.   :-5.5571   Min.   :-4.52275  
##  1st Qu.:-1.5301   1st Qu.:-1.9515   1st Qu.:-2.6954   1st Qu.:-1.30625  
##  Median :-0.3791   Median :-0.2756   Median :-0.9403   Median :-0.05940  
##  Mean   :-0.7287   Mean   :-0.3997   Mean   :-0.4989   Mean   :-0.04709  
##  3rd Qu.: 0.2639   3rd Qu.: 1.1544   3rd Qu.: 1.1164   3rd Qu.: 0.93250  
##  Max.   : 3.1263   Max.   : 3.2698   Max.   : 7.6242   Max.   : 5.01201  
##    NP_002002         NP_004487          NP_008950         NP_114172      
##  Min.   :-4.5618   Min.   :-6.26924   Min.   :-3.7523   Min.   :-3.8604  
##  1st Qu.:-1.1797   1st Qu.:-1.52702   1st Qu.:-1.9999   1st Qu.:-1.3816  
##  Median : 0.4004   Median :-0.06574   Median :-0.7266   Median :-0.4772  
##  Mean   : 0.3232   Mean   :-0.58952   Mean   :-0.4950   Mean   :-0.4398  
##  3rd Qu.: 1.7331   3rd Qu.: 1.16312   3rd Qu.: 0.7634   3rd Qu.: 0.7879  
##  Max.   : 7.7572   Max.   : 2.31641   Max.   : 3.5872   Max.   : 2.7819  
##    NP_001062         NP_057547         NP_054895         NP_001246      
##  Min.   :-4.7715   Min.   :-7.0507   Min.   :-4.1046   Min.   :-6.2690  
##  1st Qu.:-1.1492   1st Qu.:-1.7083   1st Qu.:-1.4778   1st Qu.:-1.4206  
##  Median :-0.1533   Median :-0.5469   Median :-0.3265   Median :-0.5990  
##  Mean   :-0.1275   Mean   :-0.6493   Mean   :-0.3387   Mean   :-0.5480  
##  3rd Qu.: 0.5472   3rd Qu.: 0.5915   3rd Qu.: 0.7214   3rd Qu.: 0.5243  
##  Max.   : 6.8368   Max.   : 3.0054   Max.   : 3.5856   Max.   : 3.1777  
##    NP_036451         NP_000624         NP_001159      
##  Min.   :-7.4404   Min.   :-4.2507   Min.   :-3.7622  
##  1st Qu.:-0.6950   1st Qu.:-1.3670   1st Qu.:-0.9048  
##  Median :-0.3568   Median :-0.4348   Median :-0.2071  
##  Mean   :-0.3812   Mean   :-0.4526   Mean   :-0.2972  
##  3rd Qu.: 0.5001   3rd Qu.: 0.2756   3rd Qu.: 0.4856  
##  Max.   : 3.9889   Max.   : 3.4637   Max.   : 3.4871
test_data_pam50 <- data[-samp, c(21, pam50.ind)]
summary(test_data_pam50)
##   PAM50.mRNA          NP_057427           NP_002408          NP_000415     
##  Length:21          Min.   :-2.885329   Min.   :-4.62044   Min.   :-7.450  
##  Class :character   1st Qu.:-1.015602   1st Qu.:-1.58847   1st Qu.:-3.886  
##  Mode  :character   Median : 0.106156   Median :-0.05965   Median :-2.639  
##                     Mean   : 0.001505   Mean   :-0.52519   Mean   :-1.813  
##                     3rd Qu.: 0.983817   3rd Qu.: 0.47376   3rd Qu.:-0.332  
##                     Max.   : 2.430691   Max.   : 1.88384   Max.   : 5.543  
##    NP_000413        NP_000517         NP_004439        NP_005219      
##  Min.   :-5.727   Min.   :-5.1394   Min.   :-4.805   Min.   :-5.2932  
##  1st Qu.:-4.189   1st Qu.:-2.6247   1st Qu.:-3.937   1st Qu.:-3.1028  
##  Median :-1.977   Median :-0.6412   Median :-2.766   Median :-2.1811  
##  Mean   :-1.318   Mean   :-1.1109   Mean   :-2.197   Mean   :-1.9284  
##  3rd Qu.: 0.498   3rd Qu.: 0.4757   3rd Qu.:-2.063   3rd Qu.:-0.7786  
##  Max.   : 6.038   Max.   : 3.2908   Max.   : 5.636   Max.   : 1.2458  
##    NP_058519        NP_058518       NP_001116539      NP_061155      
##  Min.   :-8.832   Min.   :-8.882   Min.   :-8.882   Min.   :-3.5251  
##  1st Qu.:-4.457   1st Qu.:-4.665   1st Qu.:-4.665   1st Qu.:-0.9938  
##  Median :-1.528   Median :-1.525   Median :-1.508   Median : 0.4276  
##  Mean   :-1.863   Mean   :-1.907   Mean   :-1.882   Mean   :-0.1099  
##  3rd Qu.: 1.543   3rd Qu.: 1.513   3rd Qu.: 1.578   3rd Qu.: 1.0702  
##  Max.   : 3.651   Max.   : 3.346   Max.   : 3.432   Max.   : 3.1565  
##   NP_001035932       NP_077006         NP_000917         NP_065178      
##  Min.   :-5.4157   Min.   :-5.4157   Min.   :-9.5520   Min.   :-1.0216  
##  1st Qu.:-1.6690   1st Qu.:-1.6690   1st Qu.:-4.4119   1st Qu.:-0.3056  
##  Median :-0.9098   Median :-0.9098   Median :-1.5420   Median : 0.3020  
##  Mean   :-0.5612   Mean   :-0.5661   Mean   :-1.9368   Mean   : 0.3318  
##  3rd Qu.: 1.2931   3rd Qu.: 1.2931   3rd Qu.: 0.5276   3rd Qu.: 0.7599  
##  Max.   : 3.5975   Max.   : 3.5975   Max.   : 4.5882   Max.   : 2.2902  
##    NP_006836          NP_006614         NP_001784         NP_006092        
##  Min.   :-3.00874   Min.   :-4.0923   Min.   :-3.6718   Min.   :-3.390196  
##  1st Qu.:-0.82783   1st Qu.:-2.4565   1st Qu.:-1.0180   1st Qu.:-1.305743  
##  Median : 0.10203   Median :-0.3891   Median :-0.1956   Median : 0.434143  
##  Mean   : 0.07189   Mean   :-0.1886   Mean   :-0.1125   Mean   :-0.000487  
##  3rd Qu.: 1.11830   3rd Qu.: 1.6648   3rd Qu.: 0.4793   3rd Qu.: 1.326765  
##  Max.   : 2.69451   Max.   : 4.7633   Max.   : 4.4598   Max.   : 2.262509  
##   NP_001153651     NP_001159403        NP_000116         NP_004314       
##  Min.   :-8.524   Min.   :-4.35843   Min.   :-7.5031   Min.   :-2.92298  
##  1st Qu.:-3.719   1st Qu.:-1.25515   1st Qu.:-2.8750   1st Qu.:-0.79335  
##  Median :-2.174   Median : 0.04056   Median :-2.2516   Median : 0.01349  
##  Mean   :-1.074   Mean   :-0.32518   Mean   :-1.8147   Mean   : 0.14324  
##  3rd Qu.: 2.243   3rd Qu.: 0.70600   3rd Qu.:-0.6479   3rd Qu.: 0.60530  
##  Max.   : 7.995   Max.   : 2.54187   Max.   : 3.8025   Max.   : 4.01700  
##    NP_060601          NP_005931          NP_003003          NP_113611       
##  Min.   :-5.43473   Min.   :-5.00931   Min.   :-5.79375   Min.   :-3.10627  
##  1st Qu.:-0.70069   1st Qu.:-1.73413   1st Qu.:-2.12534   1st Qu.:-0.87624  
##  Median : 0.07337   Median :-0.09767   Median :-0.74989   Median :-0.05761  
##  Mean   :-0.30385   Mean   :-0.31708   Mean   :-0.01564   Mean   :-0.09401  
##  3rd Qu.: 0.59385   3rd Qu.: 1.11620   3rd Qu.: 1.86016   3rd Qu.: 0.62438  
##  Max.   : 1.78540   Max.   : 2.68809   Max.   : 5.81959   Max.   : 1.69079  
##    NP_002002         NP_004487         NP_008950         NP_114172      
##  Min.   :-5.4015   Min.   :-5.9274   Min.   :-3.6807   Min.   :-3.4821  
##  1st Qu.: 0.2637   1st Qu.:-1.5020   1st Qu.:-1.6107   1st Qu.:-0.6115  
##  Median : 0.8048   Median :-0.5960   Median :-0.2357   Median : 0.8076  
##  Mean   : 0.5949   Mean   :-0.8712   Mean   :-0.2956   Mean   : 0.6668  
##  3rd Qu.: 1.6431   3rd Qu.: 0.3517   3rd Qu.: 1.0168   3rd Qu.: 2.0369  
##  Max.   : 4.1908   Max.   : 2.6384   Max.   : 3.8223   Max.   : 3.8669  
##    NP_001062           NP_057547         NP_054895         NP_001246      
##  Min.   :-3.415692   Min.   :-3.3294   Min.   :-4.0080   Min.   :-5.4615  
##  1st Qu.:-1.531180   1st Qu.:-2.1554   1st Qu.:-1.3340   1st Qu.:-1.4781  
##  Median :-0.171475   Median :-0.5776   Median : 0.4074   Median :-0.6077  
##  Mean   : 0.008234   Mean   :-0.3894   Mean   :-0.1420   Mean   :-0.7422  
##  3rd Qu.: 1.158657   3rd Qu.: 1.1069   3rd Qu.: 0.7949   3rd Qu.: 0.7382  
##  Max.   : 5.492034   Max.   : 2.8501   Max.   : 1.9232   Max.   : 2.9358  
##    NP_036451          NP_000624         NP_001159       
##  Min.   :-4.40333   Min.   :-3.4304   Min.   :-3.45513  
##  1st Qu.:-1.46064   1st Qu.:-0.9684   1st Qu.:-0.57890  
##  Median :-0.35678   Median :-0.4348   Median :-0.06175  
##  Mean   :-0.03066   Mean   :-0.7007   Mean   : 0.04626  
##  3rd Qu.: 1.93989   3rd Qu.:-0.2954   3rd Qu.: 0.99785  
##  Max.   : 4.26719   Max.   : 1.1830   Max.   : 2.27240
###test and train data barplot
train_data_pam50.plot <- train_data_pam50
train_data_pam50.plot$data <- "train_data_pam50"
test_data_pam50.plot <- test_data_pam50
test_data_pam50.plot$data <- "test_data_pam50"
train_data_pam50.plot <- t(train_data_pam50.plot)
test_data_pam50.plot <- t(test_data_pam50.plot)
data_pam50.plot <- cbind.data.frame(train_data_pam50.plot,test_data_pam50.plot)
data_pam50.plot <- t(data_pam50.plot)
data_pam50.plot <- as.data.frame(data_pam50.plot)
ggplot(data.plot, aes(x=PAM50.mRNA, fill=data)) + geom_bar() +  ggtitle("train_data (0.7) and test_data (0.3) for PAM50 proteins")

###boxplots for PAM50 proteins
data_pam50 <- rbind(train_data_pam50,test_data_pam50)
data_protein <- data_pam50[,2:length(data_pam50)]
plot_protein <- colnames(data_protein)
plot_list <- list()
for (i in seq_along(plot_protein)){ 
  plot_list[[length(plot_list)+1]]  <- ggplot(data_pam50, aes_string("PAM50.mRNA", plot_protein[i], col="PAM50.mRNA", fill="PAM50.mRNA")) + 
    geom_boxplot(alpha=0.3) + theme(axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank())
}
plot_grid(plotlist = plot_list,ncol = 1, nrow = 1) #only one (in the BC_analysis you'll find the code for all)

###violin plots for PAM50 proteins
plot_protein <- colnames(data_protein)
plot_list <- list()
for (i in seq_along(plot_protein)){ 
  plot_list[[length(plot_list)+1]]  <- ggplot(data, aes_string("PAM50.mRNA", plot_protein[i], col="PAM50.mRNA", fill="PAM50.mRNA")) + 
    geom_violin(alpha=0.3) + geom_boxplot(width=0.1) + theme(axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank())
}
plot_grid(plotlist = plot_list,ncol = 1, nrow = 1) #only one (in the BC_analysis you'll find the code for all)

Models Building

For the PAM50 data I created the same models like for data obtained by lasso regression.

Support-Vector Machine

set.seed(1)
train_control_pam50 <- trainControl(method="repeatedcv", 
                              number=3, 
                              repeats=10, 
                              savePredictions = TRUE, 
                              summaryFunction = multiClassSummary) #settng up train control for cross validation and calibration of hyperparameter
grid <- expand.grid(C = seq(0.000001,0.15,0.002)) #Tunegrid for different values of C
set.seed(1)
svm.lin.mod_pam50 <- train(PAM50.mRNA ~ ., 
                           data=train_data_pam50, 
                           trControl=train_control_pam50, 
                           method="svmLinear", 
                           preProcess = c("center","scale"), 
                           tuneGrid =grid, 
                           tuneLength = 10) #training
svm.predicts_pam50 <- predict(svm.lin.mod_pam50, 
                              newdata = test_data_pam50) #predictions on test set
confusionMatrix(svm.predicts_pam50, as.factor(test_data_pam50$PAM50.mRNA)) # confusion matrix
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             4             0         1         0
##   HER2-enriched          0             2         0         0
##   Luminal A              1             0         3         1
##   Luminal B              0             1         2         6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.7143          
##                  95% CI : (0.4782, 0.8872)
##     No Information Rate : 0.3333          
##     P-Value [Acc > NIR] : 0.0004045       
##                                           
##                   Kappa : 0.6025          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     0.8000              0.66667           0.5000
## Specificity                     0.9375              1.00000           0.8667
## Pos Pred Value                  0.8000              1.00000           0.6000
## Neg Pred Value                  0.9375              0.94737           0.8125
## Prevalence                      0.2381              0.14286           0.2857
## Detection Rate                  0.1905              0.09524           0.1429
## Detection Prevalence            0.2381              0.09524           0.2381
## Balanced Accuracy               0.8688              0.83333           0.6833
##                      Class: Luminal B
## Sensitivity                    0.8571
## Specificity                    0.7857
## Pos Pred Value                 0.6667
## Neg Pred Value                 0.9167
## Prevalence                     0.3333
## Detection Rate                 0.2857
## Detection Prevalence           0.4286
## Balanced Accuracy              0.8214

Random Forest

set.seed(1)
random.forest.mod_pam50 <- randomForest(as.factor(PAM50.mRNA) ~ ., 
                                        data=train_data_pam50, 
                                        ntree = 500, 
                                        mtry = 8, 
                                        importance = TRUE) #training
plot(random.forest.mod_pam50)

random.forest.predicts_pam50 <- predict(random.forest.mod_pam50, 
                                        newdata=test_data_pam50, 
                                        type = "class") #prediction
confusionMatrix(random.forest.predicts_pam50, as.factor(test_data_pam50$PAM50.mRNA)) #confusion matrix
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             3             0         1         0
##   HER2-enriched          1             2         0         0
##   Luminal A              1             0         3         1
##   Luminal B              0             1         2         6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.6667          
##                  95% CI : (0.4303, 0.8541)
##     No Information Rate : 0.3333          
##     P-Value [Acc > NIR] : 0.001827        
##                                           
##                   Kappa : 0.5392          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     0.6000              0.66667           0.5000
## Specificity                     0.9375              0.94444           0.8667
## Pos Pred Value                  0.7500              0.66667           0.6000
## Neg Pred Value                  0.8824              0.94444           0.8125
## Prevalence                      0.2381              0.14286           0.2857
## Detection Rate                  0.1429              0.09524           0.1429
## Detection Prevalence            0.1905              0.14286           0.2381
## Balanced Accuracy               0.7688              0.80556           0.6833
##                      Class: Luminal B
## Sensitivity                    0.8571
## Specificity                    0.7857
## Pos Pred Value                 0.6667
## Neg Pred Value                 0.9167
## Prevalence                     0.3333
## Detection Rate                 0.2857
## Detection Prevalence           0.4286
## Balanced Accuracy              0.8214

###Neural Network Classifier

neural.network.mod_pam50 <-neuralnet(as.factor(PAM50.mRNA) ~ .,          
                                    data=train_data_pam50, 
                                    hidden = c(30, 15, 8), 
                                    linear.output = FALSE,
                                    act.fct = "logistic",
                                    algorithm = 'sag')
plot(neural.network.mod_pam50,
     intercept = F,
     rep = 'best',
     col.hidden = 'darkblue', 
     col.hidden.synapse = 'black', 
     show.weights = F, 
     fill = 'lightblue',
     col.intercept  = 'red',
     fontsize = 8, 
     dimension = 15)

neural.network.mod_pam50$result.matrix #errors for model
##                                     [,1]
## error                       0.0157458185
## reached.threshold           0.0075826632
## steps                      30.0000000000
## Intercept.to.1layhid1       2.2711700284
## NP_057427.to.1layhid1       1.2222666266
## NP_002408.to.1layhid1      -1.4422921597
## NP_000415.to.1layhid1       1.3174189925
## NP_000413.to.1layhid1      -0.9337608391
## NP_000517.to.1layhid1      -1.0549317586
## NP_004439.to.1layhid1      -0.0687321781
## NP_005219.to.1layhid1      -1.8260478418
## NP_058519.to.1layhid1       1.3472872517
## NP_058518.to.1layhid1       2.4902391679
## NP_001116539.to.1layhid1    0.5181219400
## NP_061155.to.1layhid1      -0.3788395367
## NP_001035932.to.1layhid1    0.5807250700
## NP_077006.to.1layhid1       1.4538860754
## NP_000917.to.1layhid1      -0.7566860342
## NP_065178.to.1layhid1       0.0022809279
## NP_006836.to.1layhid1       0.3516447921
## NP_006614.to.1layhid1      -0.3375509717
## NP_001784.to.1layhid1       0.4000039339
## NP_006092.to.1layhid1      -1.3444814735
## NP_001153651.to.1layhid1   -1.3257465873
## NP_001159403.to.1layhid1    1.4287100744
## NP_000116.to.1layhid1       0.8460556360
## NP_004314.to.1layhid1       1.3580589499
## NP_060601.to.1layhid1      -0.0116089422
## NP_005931.to.1layhid1       2.4492027488
## NP_003003.to.1layhid1       0.9604427393
## NP_113611.to.1layhid1      -0.5153027342
## NP_002002.to.1layhid1      -0.0673333398
## NP_004487.to.1layhid1      -0.4015511751
## NP_008950.to.1layhid1       1.2008601801
## NP_114172.to.1layhid1      -0.7171655936
## NP_001062.to.1layhid1       0.6061144549
## NP_057547.to.1layhid1      -0.5410460109
## NP_054895.to.1layhid1      -1.2658825303
## NP_001246.to.1layhid1      -0.8607622148
## NP_036451.to.1layhid1       0.7111418973
## NP_000624.to.1layhid1       0.5925684592
## NP_001159.to.1layhid1      -0.0281577377
## Intercept.to.1layhid2      -0.2257338045
## NP_057427.to.1layhid2      -0.1484029455
## NP_002408.to.1layhid2      -1.4421199108
## NP_000415.to.1layhid2      -0.7403549051
## NP_000413.to.1layhid2      -0.8625422068
## NP_000517.to.1layhid2      -0.4947315008
## NP_004439.to.1layhid2       0.5095585701
## NP_005219.to.1layhid2      -1.5026134558
## NP_058519.to.1layhid2      -0.1159293040
## NP_058518.to.1layhid2       0.0277516652
## NP_001116539.to.1layhid2   -0.9128659885
## NP_061155.to.1layhid2      -0.0551891308
## NP_001035932.to.1layhid2    0.4934606022
## NP_077006.to.1layhid2       0.8569062168
## NP_000917.to.1layhid2       0.2468541031
## NP_065178.to.1layhid2      -0.7434130514
## NP_006836.to.1layhid2       0.7024928911
## NP_006614.to.1layhid2      -1.2432283098
## NP_001784.to.1layhid2       0.4703466369
## NP_006092.to.1layhid2      -0.5275990024
## NP_001153651.to.1layhid2    1.0891849762
## NP_001159403.to.1layhid2   -0.7275537405
## NP_000116.to.1layhid2      -0.1266320620
## NP_004314.to.1layhid2       0.0907649808
## NP_060601.to.1layhid2       0.2733898249
## NP_005931.to.1layhid2      -1.2082019453
## NP_003003.to.1layhid2      -3.5240971405
## NP_113611.to.1layhid2      -0.9153653753
## NP_002002.to.1layhid2      -0.2471860130
## NP_004487.to.1layhid2       0.2828275108
## NP_008950.to.1layhid2       0.8657332301
## NP_114172.to.1layhid2      -0.5576143360
## NP_001062.to.1layhid2      -1.4801214328
## NP_057547.to.1layhid2      -0.0259008501
## NP_054895.to.1layhid2       0.6275070016
## NP_001246.to.1layhid2      -0.1475513806
## NP_036451.to.1layhid2      -0.2488208797
## NP_000624.to.1layhid2      -2.0448019785
## NP_001159.to.1layhid2       0.9100781022
## Intercept.to.1layhid3      -0.7718871237
## NP_057427.to.1layhid3      -0.0266089161
## NP_002408.to.1layhid3      -1.1422367305
## NP_000415.to.1layhid3       0.7927109371
## NP_000413.to.1layhid3      -0.6092097640
## NP_000517.to.1layhid3       0.0644733912
## NP_004439.to.1layhid3       1.0778550144
## NP_005219.to.1layhid3       0.2832818129
## NP_058519.to.1layhid3      -1.2916889378
## NP_058518.to.1layhid3       2.0609851321
## NP_001116539.to.1layhid3    0.9545429920
## NP_061155.to.1layhid3       1.1782597228
## NP_001035932.to.1layhid3   -0.1144297061
## NP_077006.to.1layhid3       0.0958158845
## NP_000917.to.1layhid3       0.5770951538
## NP_065178.to.1layhid3      -1.0848854561
## NP_006836.to.1layhid3      -0.1304534436
## NP_006614.to.1layhid3       3.1929037856
## NP_001784.to.1layhid3      -1.6450623217
## NP_006092.to.1layhid3       0.7022726636
## NP_001153651.to.1layhid3   -0.6525769323
## NP_001159403.to.1layhid3    1.1688036522
## NP_000116.to.1layhid3       0.9714735057
## NP_004314.to.1layhid3      -0.0053734760
## NP_060601.to.1layhid3      -0.5500151844
## NP_005931.to.1layhid3       1.0517372002
## NP_003003.to.1layhid3      -1.7820467351
## NP_113611.to.1layhid3      -0.0668827610
## NP_002002.to.1layhid3       0.6428635402
## NP_004487.to.1layhid3       1.5671743317
## NP_008950.to.1layhid3       1.5030883232
## NP_114172.to.1layhid3       0.8605339969
## NP_001062.to.1layhid3       2.4362618668
## NP_057547.to.1layhid3      -0.6159112081
## NP_054895.to.1layhid3       1.8123405249
## NP_001246.to.1layhid3       0.4795174806
## NP_036451.to.1layhid3       0.4355233426
## NP_000624.to.1layhid3      -0.6819009085
## NP_001159.to.1layhid3      -1.0694069076
## Intercept.to.1layhid4       1.7540656292
## NP_057427.to.1layhid4      -0.3777529275
## NP_002408.to.1layhid4      -0.6039163756
## NP_000415.to.1layhid4       1.5231761378
## NP_000413.to.1layhid4      -0.0024049181
## NP_000517.to.1layhid4       0.0987706384
## NP_004439.to.1layhid4       0.7338364303
## NP_005219.to.1layhid4       1.0455370882
## NP_058519.to.1layhid4      -1.7461641169
## NP_058518.to.1layhid4       2.4505506720
## NP_001116539.to.1layhid4   -0.4519236614
## NP_061155.to.1layhid4       0.4005034325
## NP_001035932.to.1layhid4    0.4472421389
## NP_077006.to.1layhid4       0.1799411966
## NP_000917.to.1layhid4      -0.0087091528
## NP_065178.to.1layhid4      -0.6054188819
## NP_006836.to.1layhid4      -0.2464331078
## NP_006614.to.1layhid4       0.0152382926
## NP_001784.to.1layhid4       0.1274374229
## NP_006092.to.1layhid4      -0.9524170960
## NP_001153651.to.1layhid4    0.5413894125
## NP_001159403.to.1layhid4   -0.8677237342
## NP_000116.to.1layhid4      -0.9374891932
## NP_004314.to.1layhid4       0.3264878347
## NP_060601.to.1layhid4      -2.5209870308
## NP_005931.to.1layhid4      -0.6916061426
## NP_003003.to.1layhid4      -1.3689335482
## NP_113611.to.1layhid4      -0.9986406591
## NP_002002.to.1layhid4       1.6630354171
## NP_004487.to.1layhid4      -0.9811668986
## NP_008950.to.1layhid4      -1.3384134680
## NP_114172.to.1layhid4      -0.4228535282
## NP_001062.to.1layhid4      -2.8102602654
## NP_057547.to.1layhid4       1.1653855696
## NP_054895.to.1layhid4       0.5049102046
## NP_001246.to.1layhid4      -0.2282656577
## NP_036451.to.1layhid4      -0.8451617378
## NP_000624.to.1layhid4      -0.4165471811
## NP_001159.to.1layhid4      -1.3540666597
## Intercept.to.1layhid5       0.6133346750
## NP_057427.to.1layhid5      -1.7782832408
## NP_002408.to.1layhid5       2.3425369327
## NP_000415.to.1layhid5      -0.0314440396
## NP_000413.to.1layhid5      -0.1415141529
## NP_000517.to.1layhid5      -1.1230884066
## NP_004439.to.1layhid5       0.0101970680
## NP_005219.to.1layhid5       2.6143215133
## NP_058519.to.1layhid5      -1.0443471149
## NP_058518.to.1layhid5       0.6475247795
## NP_001116539.to.1layhid5    0.6162181476
## NP_061155.to.1layhid5      -0.2279475616
## NP_001035932.to.1layhid5   -0.3610340278
## NP_077006.to.1layhid5      -1.6184224188
## NP_000917.to.1layhid5      -0.7144926930
## NP_065178.to.1layhid5       1.1704863516
## NP_006836.to.1layhid5      -0.4395870160
## NP_006614.to.1layhid5       1.1957918509
## NP_001784.to.1layhid5      -0.6366817296
## NP_006092.to.1layhid5       1.1026635415
## NP_001153651.to.1layhid5   -0.5202641771
## NP_001159403.to.1layhid5   -0.8509475102
## NP_000116.to.1layhid5      -0.9027227910
## NP_004314.to.1layhid5       2.2105240022
## NP_060601.to.1layhid5      -1.0659805062
## NP_005931.to.1layhid5       1.2156751026
## NP_003003.to.1layhid5       0.1643094834
## NP_113611.to.1layhid5      -1.2581257632
## NP_002002.to.1layhid5      -0.9372373665
## NP_004487.to.1layhid5      -1.4239346733
## NP_008950.to.1layhid5      -0.9515098074
## NP_114172.to.1layhid5       1.0192877238
## NP_001062.to.1layhid5      -0.8764318050
## NP_057547.to.1layhid5      -0.1283885313
## NP_054895.to.1layhid5      -0.1763489472
## NP_001246.to.1layhid5      -0.6980680098
## NP_036451.to.1layhid5       1.0956854288
## NP_000624.to.1layhid5       0.5278810945
## NP_001159.to.1layhid5       1.2579470984
## Intercept.to.1layhid6       1.2038868386
## NP_057427.to.1layhid6      -1.1382591163
## NP_002408.to.1layhid6      -1.3076179807
## NP_000415.to.1layhid6       0.2617747120
## NP_000413.to.1layhid6      -0.2432212192
## NP_000517.to.1layhid6      -1.1683974684
## NP_004439.to.1layhid6      -0.7849272793
## NP_005219.to.1layhid6       1.7116300834
## NP_058519.to.1layhid6      -1.3099748133
## NP_058518.to.1layhid6      -0.6311863414
## NP_001116539.to.1layhid6   -0.9867369981
## NP_061155.to.1layhid6      -0.1664382758
## NP_001035932.to.1layhid6    1.9304629775
## NP_077006.to.1layhid6       0.5107457342
## NP_000917.to.1layhid6       0.2313834463
## NP_065178.to.1layhid6      -0.3056453938
## NP_006836.to.1layhid6      -0.4998757167
## NP_006614.to.1layhid6       0.5538436606
## NP_001784.to.1layhid6      -0.3396787574
## NP_006092.to.1layhid6      -1.1839620831
## NP_001153651.to.1layhid6   -0.3773506975
## NP_001159403.to.1layhid6    0.7442378720
## NP_000116.to.1layhid6      -0.0511936939
## NP_004314.to.1layhid6       0.3115385182
## NP_060601.to.1layhid6      -3.1044838952
## NP_005931.to.1layhid6      -2.0886814145
## NP_003003.to.1layhid6      -1.1614503002
## NP_113611.to.1layhid6      -0.0364646666
## NP_002002.to.1layhid6      -0.0290877739
## NP_004487.to.1layhid6      -0.1008113696
## NP_008950.to.1layhid6       0.6033015134
## NP_114172.to.1layhid6       1.0484122438
## NP_001062.to.1layhid6       0.3280714135
## NP_057547.to.1layhid6      -0.4261290144
## NP_054895.to.1layhid6      -0.8047088349
## NP_001246.to.1layhid6      -0.9428577316
## NP_036451.to.1layhid6       0.6283280135
## NP_000624.to.1layhid6       1.0932703498
## NP_001159.to.1layhid6      -3.2830722546
## Intercept.to.1layhid7      -1.0757451426
## NP_057427.to.1layhid7       0.0835728816
## NP_002408.to.1layhid7      -2.5173956589
## NP_000415.to.1layhid7      -0.1203948521
## NP_000413.to.1layhid7      -0.4095201592
## NP_000517.to.1layhid7       0.3194933243
## NP_004439.to.1layhid7       0.6012744687
## NP_005219.to.1layhid7      -0.0745515079
## NP_058519.to.1layhid7      -0.7886852371
## NP_058518.to.1layhid7       1.2794040059
## NP_001116539.to.1layhid7    2.4802170210
## NP_061155.to.1layhid7      -0.6604106317
## NP_001035932.to.1layhid7   -0.1053865349
## NP_077006.to.1layhid7       0.5283416167
## NP_000917.to.1layhid7       0.2924208814
## NP_065178.to.1layhid7       0.2143373243
## NP_006836.to.1layhid7      -0.8267811255
## NP_006614.to.1layhid7      -0.5473013088
## NP_001784.to.1layhid7       1.8326558627
## NP_006092.to.1layhid7       0.4812659769
## NP_001153651.to.1layhid7    0.7810123204
## NP_001159403.to.1layhid7   -1.4978562598
## NP_000116.to.1layhid7      -3.3252018154
## NP_004314.to.1layhid7       1.0054219095
## NP_060601.to.1layhid7      -0.3306661427
## NP_005931.to.1layhid7       0.5812623170
## NP_003003.to.1layhid7       0.2638388659
## NP_113611.to.1layhid7      -2.6043238145
## NP_002002.to.1layhid7      -0.5353211357
## NP_004487.to.1layhid7       2.3572789744
## NP_008950.to.1layhid7       0.4476646073
## NP_114172.to.1layhid7       0.6243629199
## NP_001062.to.1layhid7      -1.2140858328
## NP_057547.to.1layhid7       2.5640440871
## NP_054895.to.1layhid7       0.7164874014
## NP_001246.to.1layhid7       0.6024743868
## NP_036451.to.1layhid7       2.8187125850
## NP_000624.to.1layhid7       0.9945456566
## NP_001159.to.1layhid7      -0.8105181337
## Intercept.to.1layhid8       0.0552873087
## NP_057427.to.1layhid8      -1.5427253222
## NP_002408.to.1layhid8       0.3738872617
## NP_000415.to.1layhid8       0.5905895380
## NP_000413.to.1layhid8       1.0069745325
## NP_000517.to.1layhid8      -0.7657748783
## NP_004439.to.1layhid8       1.1092723570
## NP_005219.to.1layhid8      -1.2490553034
## NP_058519.to.1layhid8       1.6237804861
## NP_058518.to.1layhid8       0.4761185127
## NP_001116539.to.1layhid8    1.4394501947
## NP_061155.to.1layhid8      -0.2491608283
## NP_001035932.to.1layhid8   -0.8951637977
## NP_077006.to.1layhid8       2.1015734788
## NP_000917.to.1layhid8       1.4569038575
## NP_065178.to.1layhid8       0.9784200214
## NP_006836.to.1layhid8       1.9588204828
## NP_006614.to.1layhid8       0.3064052294
## NP_001784.to.1layhid8       1.3520675715
## NP_006092.to.1layhid8      -0.5722046756
## NP_001153651.to.1layhid8    1.0191381294
## NP_001159403.to.1layhid8   -2.2272945981
## NP_000116.to.1layhid8       0.7817457193
## NP_004314.to.1layhid8       1.7828135316
## NP_060601.to.1layhid8       1.0010580409
## NP_005931.to.1layhid8      -1.2209550565
## NP_003003.to.1layhid8       0.8887679273
## NP_113611.to.1layhid8      -1.0859247565
## NP_002002.to.1layhid8      -0.5698605898
## NP_004487.to.1layhid8      -1.1458644071
## NP_008950.to.1layhid8      -1.8782906117
## NP_114172.to.1layhid8       0.4521799475
## NP_001062.to.1layhid8      -0.5260380410
## NP_057547.to.1layhid8      -0.1639560656
## NP_054895.to.1layhid8      -0.0778705632
## NP_001246.to.1layhid8       0.6061631859
## NP_036451.to.1layhid8       1.6669157910
## NP_000624.to.1layhid8      -0.5002204783
## NP_001159.to.1layhid8      -0.4681492936
## Intercept.to.1layhid9      -1.2051619920
## NP_057427.to.1layhid9       0.3992172265
## NP_002408.to.1layhid9      -0.4169661785
## NP_000415.to.1layhid9       0.9768595395
## NP_000413.to.1layhid9       2.8815730527
## NP_000517.to.1layhid9       0.3992334804
## NP_004439.to.1layhid9      -0.7788535935
## NP_005219.to.1layhid9      -0.4336742464
## NP_058519.to.1layhid9      -0.1387314995
## NP_058518.to.1layhid9       0.7951080337
## NP_001116539.to.1layhid9    0.4621594644
## NP_061155.to.1layhid9      -0.1504604411
## NP_001035932.to.1layhid9   -0.1246624213
## NP_077006.to.1layhid9      -0.2945708324
## NP_000917.to.1layhid9       0.8191372184
## NP_065178.to.1layhid9      -0.3071850940
## NP_006836.to.1layhid9       0.1019700347
## NP_006614.to.1layhid9       0.6930303371
## NP_001784.to.1layhid9      -1.0073871460
## NP_006092.to.1layhid9       1.7899648127
## NP_001153651.to.1layhid9   -0.3193575531
## NP_001159403.to.1layhid9   -1.0015044078
## NP_000116.to.1layhid9      -0.5351234565
## NP_004314.to.1layhid9       1.7353892496
## NP_060601.to.1layhid9       1.4495858054
## NP_005931.to.1layhid9       0.3186664338
## NP_003003.to.1layhid9       0.5503602508
## NP_113611.to.1layhid9       0.2877405245
## NP_002002.to.1layhid9      -0.4305257319
## NP_004487.to.1layhid9       0.1985149868
## NP_008950.to.1layhid9      -1.4185519675
## NP_114172.to.1layhid9       0.6100004058
## NP_001062.to.1layhid9      -0.0130870655
## NP_057547.to.1layhid9      -0.7177943341
## NP_054895.to.1layhid9       2.2696861128
## NP_001246.to.1layhid9      -0.1835660420
## NP_036451.to.1layhid9       0.4900022403
## NP_000624.to.1layhid9      -0.3921461889
## NP_001159.to.1layhid9       1.5154928783
## Intercept.to.1layhid10     -1.0635794388
## NP_057427.to.1layhid10     -0.5929337996
## NP_002408.to.1layhid10     -1.2978765944
## NP_000415.to.1layhid10     -1.4349033422
## NP_000413.to.1layhid10      1.0679086254
## NP_000517.to.1layhid10     -0.4373139539
## NP_004439.to.1layhid10     -0.9941685191
## NP_005219.to.1layhid10      0.6495013161
## NP_058519.to.1layhid10     -0.1517516766
## NP_058518.to.1layhid10      0.2062339211
## NP_001116539.to.1layhid10  -0.1580366677
## NP_061155.to.1layhid10     -0.2212020260
## NP_001035932.to.1layhid10   0.8716104403
## NP_077006.to.1layhid10     -0.6793998230
## NP_000917.to.1layhid10      1.2517187413
## NP_065178.to.1layhid10     -0.1966123235
## NP_006836.to.1layhid10     -0.0300689845
## NP_006614.to.1layhid10      0.3436421273
## NP_001784.to.1layhid10     -2.1202457134
## NP_006092.to.1layhid10     -1.0926693861
## NP_001153651.to.1layhid10   0.3871627402
## NP_001159403.to.1layhid10  -0.9047627186
## NP_000116.to.1layhid10      1.0600079816
## NP_004314.to.1layhid10      1.2714100536
## NP_060601.to.1layhid10      1.5500936683
## NP_005931.to.1layhid10     -0.7086976084
## NP_003003.to.1layhid10     -1.1201660458
## NP_113611.to.1layhid10     -0.7064529273
## NP_002002.to.1layhid10      1.0830597526
## NP_004487.to.1layhid10     -0.7687800693
## NP_008950.to.1layhid10      0.9085873241
## NP_114172.to.1layhid10     -1.2729999954
## NP_001062.to.1layhid10      1.2920698833
## NP_057547.to.1layhid10     -0.7240824623
## NP_054895.to.1layhid10     -0.5882002829
## NP_001246.to.1layhid10     -0.2722111925
## NP_036451.to.1layhid10      1.5777318913
## NP_000624.to.1layhid10      0.9196915005
## NP_001159.to.1layhid10     -0.6280400439
## Intercept.to.1layhid11      0.7877451629
## NP_057427.to.1layhid11      0.2514446072
## NP_002408.to.1layhid11      0.4961758162
## NP_000415.to.1layhid11      0.6774739792
## NP_000413.to.1layhid11      1.3472510076
## NP_000517.to.1layhid11     -1.0570061701
## NP_004439.to.1layhid11     -0.5002370479
## NP_005219.to.1layhid11     -1.6960170937
## NP_058519.to.1layhid11     -2.1489963048
## NP_058518.to.1layhid11      0.4260198636
## NP_001116539.to.1layhid11   0.3684898048
## NP_061155.to.1layhid11      0.0144047489
## NP_001035932.to.1layhid11  -0.9308787733
## NP_077006.to.1layhid11     -2.1252703921
## NP_000917.to.1layhid11      1.5179267465
## NP_065178.to.1layhid11     -0.3193741163
## NP_006836.to.1layhid11      0.1601328781
## NP_006614.to.1layhid11     -0.5118840122
## NP_001784.to.1layhid11      1.2704534915
## NP_006092.to.1layhid11     -1.8661989610
## NP_001153651.to.1layhid11  -0.2254393776
## NP_001159403.to.1layhid11  -0.9200990892
## NP_000116.to.1layhid11     -0.0406236555
## NP_004314.to.1layhid11      1.2784048291
## NP_060601.to.1layhid11     -1.1470833720
## NP_005931.to.1layhid11     -1.4297386493
## NP_003003.to.1layhid11     -0.4478469724
## NP_113611.to.1layhid11     -1.0180231044
## NP_002002.to.1layhid11      0.0908693751
## NP_004487.to.1layhid11     -0.2168684199
## NP_008950.to.1layhid11     -0.6632731496
## NP_114172.to.1layhid11      0.8376178912
## NP_001062.to.1layhid11     -0.5357665405
## NP_057547.to.1layhid11     -0.2237478109
## NP_054895.to.1layhid11     -1.2120068917
## NP_001246.to.1layhid11      0.8399076969
## NP_036451.to.1layhid11      1.4008761075
## NP_000624.to.1layhid11     -0.0428619305
## NP_001159.to.1layhid11     -2.3307852316
## Intercept.to.1layhid12     -0.5767782855
## NP_057427.to.1layhid12      0.7502462806
## NP_002408.to.1layhid12     -0.9021437314
## NP_000415.to.1layhid12     -1.7051373796
## NP_000413.to.1layhid12     -0.3089619362
## NP_000517.to.1layhid12     -1.1518855258
## NP_004439.to.1layhid12      0.3490246128
## NP_005219.to.1layhid12      0.5584185261
## NP_058519.to.1layhid12      1.3792237785
## NP_058518.to.1layhid12     -0.1249590356
## NP_001116539.to.1layhid12   0.4434468105
## NP_061155.to.1layhid12      0.9785208426
## NP_001035932.to.1layhid12  -0.2970010080
## NP_077006.to.1layhid12      1.1055444337
## NP_000917.to.1layhid12      0.5665370374
## NP_065178.to.1layhid12      1.1587046924
## NP_006836.to.1layhid12      0.0249894236
## NP_006614.to.1layhid12     -0.1182339615
## NP_001784.to.1layhid12     -0.0324638599
## NP_006092.to.1layhid12     -0.3240624614
## NP_001153651.to.1layhid12  -0.1766306686
## NP_001159403.to.1layhid12  -3.0932991490
## NP_000116.to.1layhid12     -1.1861432266
## NP_004314.to.1layhid12      0.0700867296
## NP_060601.to.1layhid12     -0.2223965927
## NP_005931.to.1layhid12     -0.7582517360
## NP_003003.to.1layhid12     -2.1436943314
## NP_113611.to.1layhid12      0.6108408118
## NP_002002.to.1layhid12      0.4963872334
## NP_004487.to.1layhid12      1.2719551297
## NP_008950.to.1layhid12      0.9929203126
## NP_114172.to.1layhid12      0.6781969476
## NP_001062.to.1layhid12      0.6928044980
## NP_057547.to.1layhid12     -0.0063159164
## NP_054895.to.1layhid12      1.5077680965
## NP_001246.to.1layhid12      2.1762068169
## NP_036451.to.1layhid12     -1.1422598375
## NP_000624.to.1layhid12      0.0290694360
## NP_001159.to.1layhid12      0.3593292150
## Intercept.to.1layhid13      1.7463921628
## NP_057427.to.1layhid13      0.4116776363
## NP_002408.to.1layhid13      0.5133998396
## NP_000415.to.1layhid13      1.6331279036
## NP_000413.to.1layhid13     -2.3569630385
## NP_000517.to.1layhid13     -2.9881072857
## NP_004439.to.1layhid13     -1.7186765711
## NP_005219.to.1layhid13     -0.9517725272
## NP_058519.to.1layhid13      1.8861129165
## NP_058518.to.1layhid13      2.5217181035
## NP_001116539.to.1layhid13  -0.5125220741
## NP_061155.to.1layhid13     -1.1549761443
## NP_001035932.to.1layhid13  -0.6693478719
## NP_077006.to.1layhid13     -0.1619915939
## NP_000917.to.1layhid13      0.3381362601
## NP_065178.to.1layhid13      2.0628138950
## NP_006836.to.1layhid13      0.4871476450
## NP_006614.to.1layhid13     -0.1516467014
## NP_001784.to.1layhid13     -1.3457153413
## NP_006092.to.1layhid13      0.4604353980
## NP_001153651.to.1layhid13   0.1688397942
## NP_001159403.to.1layhid13   0.6370541898
## NP_000116.to.1layhid13      0.0524702344
## NP_004314.to.1layhid13     -1.3439440349
## NP_060601.to.1layhid13      0.5730302394
## NP_005931.to.1layhid13      0.0729526185
## NP_003003.to.1layhid13     -1.2205240052
## NP_113611.to.1layhid13      1.7803818779
## NP_002002.to.1layhid13     -0.3146610824
## NP_004487.to.1layhid13      1.0623465160
## NP_008950.to.1layhid13     -0.2846448039
## NP_114172.to.1layhid13     -0.2958534709
## NP_001062.to.1layhid13     -0.9277367415
## NP_057547.to.1layhid13      1.3993850424
## NP_054895.to.1layhid13      2.4679067366
## NP_001246.to.1layhid13      1.4931950256
## NP_036451.to.1layhid13      1.3765034564
## NP_000624.to.1layhid13      0.2589024108
## NP_001159.to.1layhid13      1.3289344585
## Intercept.to.1layhid14      0.2188227951
## NP_057427.to.1layhid14      0.1815537329
## NP_002408.to.1layhid14      0.2215493703
## NP_000415.to.1layhid14      1.5908851538
## NP_000413.to.1layhid14      1.6219688161
## NP_000517.to.1layhid14      0.7801209996
## NP_004439.to.1layhid14     -0.5806318328
## NP_005219.to.1layhid14     -0.7631717454
## NP_058519.to.1layhid14     -1.2845893942
## NP_058518.to.1layhid14      0.4259783022
## NP_001116539.to.1layhid14   0.9426348263
## NP_061155.to.1layhid14      0.5689745477
## NP_001035932.to.1layhid14  -1.5387501959
## NP_077006.to.1layhid14     -1.3339282793
## NP_000917.to.1layhid14      0.3084058854
## NP_065178.to.1layhid14     -1.1893228589
## NP_006836.to.1layhid14     -0.4292224916
## NP_006614.to.1layhid14     -0.5846271146
## NP_001784.to.1layhid14      0.7939008383
## NP_006092.to.1layhid14      0.9838030083
## NP_001153651.to.1layhid14  -1.9848642602
## NP_001159403.to.1layhid14   1.0677535714
## NP_000116.to.1layhid14     -0.7737142545
## NP_004314.to.1layhid14      0.0481722771
## NP_060601.to.1layhid14     -0.5785493663
## NP_005931.to.1layhid14     -1.5420683106
## NP_003003.to.1layhid14      2.2610478065
## NP_113611.to.1layhid14     -0.0462037869
## NP_002002.to.1layhid14      0.9646477499
## NP_004487.to.1layhid14      0.0506379887
## NP_008950.to.1layhid14      0.9345333719
## NP_114172.to.1layhid14     -0.0622675330
## NP_001062.to.1layhid14      0.1569287449
## NP_057547.to.1layhid14      1.1180979940
## NP_054895.to.1layhid14      1.6736256425
## NP_001246.to.1layhid14      0.1927955367
## NP_036451.to.1layhid14      1.1347665805
## NP_000624.to.1layhid14     -0.9793781787
## NP_001159.to.1layhid14     -0.0010306766
## Intercept.to.1layhid15      2.0748649424
## NP_057427.to.1layhid15      1.0009647691
## NP_002408.to.1layhid15      0.7886313484
## NP_000415.to.1layhid15      0.3736475958
## NP_000413.to.1layhid15      0.2395435035
## NP_000517.to.1layhid15     -1.2718989847
## NP_004439.to.1layhid15      0.4195135114
## NP_005219.to.1layhid15     -0.4321716007
## NP_058519.to.1layhid15     -0.7080717763
## NP_058518.to.1layhid15      0.4199207619
## NP_001116539.to.1layhid15  -0.5688352861
## NP_061155.to.1layhid15      1.1656040147
## NP_001035932.to.1layhid15   1.0644985968
## NP_077006.to.1layhid15      2.1565060407
## NP_000917.to.1layhid15      0.5101750560
## NP_065178.to.1layhid15      1.0501729617
## NP_006836.to.1layhid15      3.2819329719
## NP_006614.to.1layhid15     -0.8763049347
## NP_001784.to.1layhid15      0.0515338500
## NP_006092.to.1layhid15      0.0310391418
## NP_001153651.to.1layhid15   1.4366055917
## NP_001159403.to.1layhid15  -0.0475017442
## NP_000116.to.1layhid15      2.7045011084
## NP_004314.to.1layhid15      0.8229477985
## NP_060601.to.1layhid15     -0.2659976732
## NP_005931.to.1layhid15     -0.7191951080
## NP_003003.to.1layhid15     -0.6453201277
## NP_113611.to.1layhid15      0.0098887472
## NP_002002.to.1layhid15      0.9426381643
## NP_004487.to.1layhid15      1.4651922988
## NP_008950.to.1layhid15     -1.7614011061
## NP_114172.to.1layhid15     -0.9330432895
## NP_001062.to.1layhid15      0.2672778318
## NP_057547.to.1layhid15     -0.0928145460
## NP_054895.to.1layhid15      0.5248408958
## NP_001246.to.1layhid15      1.0542650966
## NP_036451.to.1layhid15      0.9675007810
## NP_000624.to.1layhid15      1.5407417744
## NP_001159.to.1layhid15     -0.6931446276
## Intercept.to.1layhid16      1.0323943505
## NP_057427.to.1layhid16      0.4285420870
## NP_002408.to.1layhid16      0.0435073694
## NP_000415.to.1layhid16      0.2378426224
## NP_000413.to.1layhid16      0.5303833437
## NP_000517.to.1layhid16      0.6850843320
## NP_004439.to.1layhid16     -0.3867059928
## NP_005219.to.1layhid16      1.7476834711
## NP_058519.to.1layhid16     -0.7885285879
## NP_058518.to.1layhid16     -1.1441955252
## NP_001116539.to.1layhid16  -0.5600278500
## NP_061155.to.1layhid16      2.4431391193
## NP_001035932.to.1layhid16  -0.2510970612
## NP_077006.to.1layhid16      0.5697922688
## NP_000917.to.1layhid16      2.3484237708
## NP_065178.to.1layhid16     -0.1288609091
## NP_006836.to.1layhid16      0.2148654620
## NP_006614.to.1layhid16     -0.4639502454
## NP_001784.to.1layhid16      0.7455663056
## NP_006092.to.1layhid16      0.0118072826
## NP_001153651.to.1layhid16   0.1817585395
## NP_001159403.to.1layhid16   1.1508368643
## NP_000116.to.1layhid16     -0.5683201725
## NP_004314.to.1layhid16     -0.0269673088
## NP_060601.to.1layhid16      0.7562563992
## NP_005931.to.1layhid16     -0.4424236654
## NP_003003.to.1layhid16      0.4243507278
## NP_113611.to.1layhid16     -1.0242415019
## NP_002002.to.1layhid16     -0.7395268696
## NP_004487.to.1layhid16      0.3144994377
## NP_008950.to.1layhid16      0.4907711995
## NP_114172.to.1layhid16      1.4190137006
## NP_001062.to.1layhid16      1.8307351002
## NP_057547.to.1layhid16     -2.3849370896
## NP_054895.to.1layhid16     -0.8007318201
## NP_001246.to.1layhid16     -0.2078183251
## NP_036451.to.1layhid16     -0.0531589804
## NP_000624.to.1layhid16      0.9491539458
## NP_001159.to.1layhid16      2.2096186389
## Intercept.to.1layhid17     -1.7834402950
## NP_057427.to.1layhid17     -0.2031739465
## NP_002408.to.1layhid17     -1.5654973075
## NP_000415.to.1layhid17      0.1855832770
## NP_000413.to.1layhid17     -0.1846334559
## NP_000517.to.1layhid17      0.9185991574
## NP_004439.to.1layhid17      1.1177254833
## NP_005219.to.1layhid17      0.1725871491
## NP_058519.to.1layhid17      0.8557310135
## NP_058518.to.1layhid17      0.6209072910
## NP_001116539.to.1layhid17   0.1157647113
## NP_061155.to.1layhid17     -1.6794867823
## NP_001035932.to.1layhid17   0.0883047505
## NP_077006.to.1layhid17     -1.1813024725
## NP_000917.to.1layhid17      0.2930490647
## NP_065178.to.1layhid17     -0.8688765147
## NP_006836.to.1layhid17     -0.1116208182
## NP_006614.to.1layhid17      1.0562396352
## NP_001784.to.1layhid17     -0.7722770671
## NP_006092.to.1layhid17     -0.8801270402
## NP_001153651.to.1layhid17   0.9734032802
## NP_001159403.to.1layhid17   1.5466393599
## NP_000116.to.1layhid17      0.6594499107
## NP_004314.to.1layhid17     -0.5070831048
## NP_060601.to.1layhid17      0.7741824114
## NP_005931.to.1layhid17     -0.2405140541
## NP_003003.to.1layhid17     -0.0127377641
## NP_113611.to.1layhid17      0.0103108848
## NP_002002.to.1layhid17     -2.2840294473
## NP_004487.to.1layhid17     -0.1716360883
## NP_008950.to.1layhid17      0.7389882382
## NP_114172.to.1layhid17      1.0070606709
## NP_001062.to.1layhid17     -0.5682606947
## NP_057547.to.1layhid17      0.7849028881
## NP_054895.to.1layhid17     -1.5341465825
## NP_001246.to.1layhid17      2.1288188976
## NP_036451.to.1layhid17     -1.4185643873
## NP_000624.to.1layhid17      0.2078547202
## NP_001159.to.1layhid17     -1.2990079728
## Intercept.to.1layhid18      0.4553756368
## NP_057427.to.1layhid18     -2.0059006348
## NP_002408.to.1layhid18     -0.9486015024
## NP_000415.to.1layhid18      0.4500488154
## NP_000413.to.1layhid18     -0.9305600750
## NP_000517.to.1layhid18     -0.7278584410
## NP_004439.to.1layhid18     -1.4909911683
## NP_005219.to.1layhid18     -0.3078867528
## NP_058519.to.1layhid18     -1.1741825454
## NP_058518.to.1layhid18     -0.7737607665
## NP_001116539.to.1layhid18   1.6817156218
## NP_061155.to.1layhid18      0.8903108899
## NP_001035932.to.1layhid18   0.2810635267
## NP_077006.to.1layhid18     -1.5986120836
## NP_000917.to.1layhid18      0.9039934754
## NP_065178.to.1layhid18     -0.3026242336
## NP_006836.to.1layhid18     -0.0740760027
## NP_006614.to.1layhid18     -0.5129607686
## NP_001784.to.1layhid18      0.4231429839
## NP_006092.to.1layhid18      0.2367802899
## NP_001153651.to.1layhid18   1.2204539051
## NP_001159403.to.1layhid18  -0.2546628611
## NP_000116.to.1layhid18      0.4104269538
## NP_004314.to.1layhid18     -1.3904799070
## NP_060601.to.1layhid18     -0.2132083662
## NP_005931.to.1layhid18     -1.7294632666
## NP_003003.to.1layhid18      1.2963444343
## NP_113611.to.1layhid18      0.4946625096
## NP_002002.to.1layhid18      0.3339106987
## NP_004487.to.1layhid18     -0.6070738718
## NP_008950.to.1layhid18      2.4509793255
## NP_114172.to.1layhid18     -0.5403828776
## NP_001062.to.1layhid18     -1.3353255044
## NP_057547.to.1layhid18     -0.5478592258
## NP_054895.to.1layhid18     -2.2426422829
## NP_001246.to.1layhid18     -0.0696655931
## NP_036451.to.1layhid18     -1.0789213729
## NP_000624.to.1layhid18     -0.5379504487
## NP_001159.to.1layhid18     -1.0099497846
## Intercept.to.1layhid19     -1.1043875230
## NP_057427.to.1layhid19     -0.5851986531
## NP_002408.to.1layhid19      2.3110090817
## NP_000415.to.1layhid19     -0.4562074212
## NP_000413.to.1layhid19      0.4592913795
## NP_000517.to.1layhid19      1.1634268874
## NP_004439.to.1layhid19      0.0566731844
## NP_005219.to.1layhid19     -0.3389082987
## NP_058519.to.1layhid19      1.0384279240
## NP_058518.to.1layhid19      0.9437941548
## NP_001116539.to.1layhid19   1.0833554115
## NP_061155.to.1layhid19      1.4927010600
## NP_001035932.to.1layhid19   0.4978765150
## NP_077006.to.1layhid19     -0.5286894512
## NP_000917.to.1layhid19      2.2080803435
## NP_065178.to.1layhid19      0.0536407682
## NP_006836.to.1layhid19     -2.0979493752
## NP_006614.to.1layhid19     -0.6302012558
## NP_001784.to.1layhid19     -0.5799329548
## NP_006092.to.1layhid19     -4.5060801752
## NP_001153651.to.1layhid19  -1.8093349590
## NP_001159403.to.1layhid19   0.1446788809
## NP_000116.to.1layhid19      1.4648926615
## NP_004314.to.1layhid19      0.5344329262
## NP_060601.to.1layhid19      0.4876060537
## NP_005931.to.1layhid19      0.0938547007
## NP_003003.to.1layhid19     -0.6538579862
## NP_113611.to.1layhid19     -0.7961495919
## NP_002002.to.1layhid19      1.9754986563
## NP_004487.to.1layhid19      0.4786819730
## NP_008950.to.1layhid19      0.1852022205
## NP_114172.to.1layhid19      0.4412129293
## NP_001062.to.1layhid19     -0.6387007310
## NP_057547.to.1layhid19      1.7990209291
## NP_054895.to.1layhid19      0.6094715593
## NP_001246.to.1layhid19     -0.3227816739
## NP_036451.to.1layhid19     -0.4308299447
## NP_000624.to.1layhid19     -1.4638833150
## NP_001159.to.1layhid19      0.1508439874
## Intercept.to.1layhid20      1.2349334594
## NP_057427.to.1layhid20      0.1757168376
## NP_002408.to.1layhid20      1.1675608488
## NP_000415.to.1layhid20      0.8174573418
## NP_000413.to.1layhid20      1.6594075056
## NP_000517.to.1layhid20      0.3691313459
## NP_004439.to.1layhid20      0.9340447099
## NP_005219.to.1layhid20      0.3333195124
## NP_058519.to.1layhid20     -0.0482167330
## NP_058518.to.1layhid20     -0.2246032348
## NP_001116539.to.1layhid20   0.5820416854
## NP_061155.to.1layhid20     -0.4696270471
## NP_001035932.to.1layhid20   0.5830847170
## NP_077006.to.1layhid20     -1.6757031609
## NP_000917.to.1layhid20     -0.3200350111
## NP_065178.to.1layhid20      0.6544764513
## NP_006836.to.1layhid20     -0.5886357890
## NP_006614.to.1layhid20      0.6573348003
## NP_001784.to.1layhid20      1.8416891349
## NP_006092.to.1layhid20      0.3225296513
## NP_001153651.to.1layhid20   0.4555927529
## NP_001159403.to.1layhid20   0.9350909339
## NP_000116.to.1layhid20     -2.6605833960
## NP_004314.to.1layhid20     -0.3588649396
## NP_060601.to.1layhid20     -0.4703164076
## NP_005931.to.1layhid20     -1.4507548476
## NP_003003.to.1layhid20      0.2116173709
## NP_113611.to.1layhid20      1.5914253517
## NP_002002.to.1layhid20      0.4977825503
## NP_004487.to.1layhid20     -0.7504064443
## NP_008950.to.1layhid20      0.9735316169
## NP_114172.to.1layhid20      2.7557924359
## NP_001062.to.1layhid20      0.2923471557
## NP_057547.to.1layhid20     -0.0348292789
## NP_054895.to.1layhid20      0.1461346782
## NP_001246.to.1layhid20      0.1690058878
## NP_036451.to.1layhid20     -1.1044307864
## NP_000624.to.1layhid20      0.1046379229
## NP_001159.to.1layhid20      0.5085406076
## Intercept.to.1layhid21     -0.2431558982
## NP_057427.to.1layhid21     -0.2872032952
## NP_002408.to.1layhid21     -1.7161493985
## NP_000415.to.1layhid21      0.7157750543
## NP_000413.to.1layhid21      1.2275047558
## NP_000517.to.1layhid21     -0.1607537911
## NP_004439.to.1layhid21     -2.2661831779
## NP_005219.to.1layhid21      1.0320151454
## NP_058519.to.1layhid21      0.6048144134
## NP_058518.to.1layhid21      1.0341911836
## NP_001116539.to.1layhid21  -0.3835033729
## NP_061155.to.1layhid21      0.0161048524
## NP_001035932.to.1layhid21   0.8147029904
## NP_077006.to.1layhid21     -1.1871278420
## NP_000917.to.1layhid21     -0.4281529431
## NP_065178.to.1layhid21      0.4322640024
## NP_006836.to.1layhid21     -0.2770209839
## NP_006614.to.1layhid21     -1.5891375016
## NP_001784.to.1layhid21     -2.8520434744
## NP_006092.to.1layhid21     -1.9426706321
## NP_001153651.to.1layhid21   0.0827350087
## NP_001159403.to.1layhid21   0.4172975116
## NP_000116.to.1layhid21      0.7059892732
## NP_004314.to.1layhid21      2.8208300540
## NP_060601.to.1layhid21     -1.8737789272
## NP_005931.to.1layhid21     -0.1843129667
## NP_003003.to.1layhid21      0.4660298964
## NP_113611.to.1layhid21     -0.9635362279
## NP_002002.to.1layhid21      1.7012440397
## NP_004487.to.1layhid21      0.4397172704
## NP_008950.to.1layhid21     -0.1136010697
## NP_114172.to.1layhid21      0.1575528611
## NP_001062.to.1layhid21     -0.7585763399
## NP_057547.to.1layhid21     -0.8314305196
## NP_054895.to.1layhid21     -2.0069749151
## NP_001246.to.1layhid21      2.3729034097
## NP_036451.to.1layhid21      1.2082551323
## NP_000624.to.1layhid21      0.5190862338
## NP_001159.to.1layhid21     -1.7782175997
## Intercept.to.1layhid22      0.0322099215
## NP_057427.to.1layhid22      0.0154860711
## NP_002408.to.1layhid22      1.3014704474
## NP_000415.to.1layhid22     -0.4147182140
## NP_000413.to.1layhid22     -0.7892387287
## NP_000517.to.1layhid22      0.3411229617
## NP_004439.to.1layhid22      0.2118966212
## NP_005219.to.1layhid22     -0.8183843332
## NP_058519.to.1layhid22     -0.7399105344
## NP_058518.to.1layhid22     -0.2476548716
## NP_001116539.to.1layhid22   0.0300069350
## NP_061155.to.1layhid22      0.7148668544
## NP_001035932.to.1layhid22   1.7297887187
## NP_077006.to.1layhid22      3.3662187150
## NP_000917.to.1layhid22      1.6369355653
## NP_065178.to.1layhid22      1.9255484014
## NP_006836.to.1layhid22     -1.5016973391
## NP_006614.to.1layhid22     -2.6159217252
## NP_001784.to.1layhid22     -1.0108454999
## NP_006092.to.1layhid22      1.7717899239
## NP_001153651.to.1layhid22   1.8156014096
## NP_001159403.to.1layhid22  -0.6354275756
## NP_000116.to.1layhid22     -0.2963960313
## NP_004314.to.1layhid22     -1.7883871531
## NP_060601.to.1layhid22     -0.5449676372
## NP_005931.to.1layhid22      1.3933571993
## NP_003003.to.1layhid22     -0.0447792792
## NP_113611.to.1layhid22     -1.2899390857
## NP_002002.to.1layhid22      0.0912523055
## NP_004487.to.1layhid22      0.0286921989
## NP_008950.to.1layhid22     -0.9005590288
## NP_114172.to.1layhid22     -1.1517342577
## NP_001062.to.1layhid22     -0.7072079700
## NP_057547.to.1layhid22     -1.7195983016
## NP_054895.to.1layhid22      1.4065934728
## NP_001246.to.1layhid22      0.5843878579
## NP_036451.to.1layhid22      0.0394386945
## NP_000624.to.1layhid22      0.3871748552
## NP_001159.to.1layhid22      0.1894667020
## Intercept.to.1layhid23     -0.3175193916
## NP_057427.to.1layhid23      2.9630226732
## NP_002408.to.1layhid23     -0.6288972213
## NP_000415.to.1layhid23     -1.5190497828
## NP_000413.to.1layhid23     -1.0596964156
## NP_000517.to.1layhid23     -0.1745685305
## NP_004439.to.1layhid23     -0.6179566773
## NP_005219.to.1layhid23     -0.9022441957
## NP_058519.to.1layhid23      0.4018060232
## NP_058518.to.1layhid23      0.4438234756
## NP_001116539.to.1layhid23   0.9890106632
## NP_061155.to.1layhid23      0.1868312887
## NP_001035932.to.1layhid23   0.3888894312
## NP_077006.to.1layhid23     -2.0170927516
## NP_000917.to.1layhid23     -0.9675676773
## NP_065178.to.1layhid23     -0.1685004443
## NP_006836.to.1layhid23      0.9281519980
## NP_006614.to.1layhid23      0.7586807453
## NP_001784.to.1layhid23      0.3834394364
## NP_006092.to.1layhid23     -0.9568173268
## NP_001153651.to.1layhid23  -1.0490373614
## NP_001159403.to.1layhid23   1.3121989061
## NP_000116.to.1layhid23     -0.1331474859
## NP_004314.to.1layhid23     -0.0328011152
## NP_060601.to.1layhid23      0.5222236274
## NP_005931.to.1layhid23     -0.0704653304
## NP_003003.to.1layhid23     -0.2666131767
## NP_113611.to.1layhid23      0.3428440429
## NP_002002.to.1layhid23     -1.2592008510
## NP_004487.to.1layhid23     -0.5612995484
## NP_008950.to.1layhid23      0.6281557291
## NP_114172.to.1layhid23      0.1397341680
## NP_001062.to.1layhid23     -0.1899687182
## NP_057547.to.1layhid23     -1.6265970432
## NP_054895.to.1layhid23     -1.0926057177
## NP_001246.to.1layhid23     -0.5701779940
## NP_036451.to.1layhid23     -0.3005565803
## NP_000624.to.1layhid23      0.6464732318
## NP_001159.to.1layhid23      0.3665784914
## Intercept.to.1layhid24     -1.3705264310
## NP_057427.to.1layhid24      0.5108399988
## NP_002408.to.1layhid24      1.3806102838
## NP_000415.to.1layhid24      0.3316214698
## NP_000413.to.1layhid24     -0.4710927445
## NP_000517.to.1layhid24      1.9876536165
## NP_004439.to.1layhid24      0.2233587468
## NP_005219.to.1layhid24      0.4753304566
## NP_058519.to.1layhid24      0.0672787344
## NP_058518.to.1layhid24      0.1734980089
## NP_001116539.to.1layhid24  -1.8084307003
## NP_061155.to.1layhid24     -1.0086289356
## NP_001035932.to.1layhid24   0.5666874540
## NP_077006.to.1layhid24      0.2071733866
## NP_000917.to.1layhid24     -1.2188822350
## NP_065178.to.1layhid24     -2.0886941954
## NP_006836.to.1layhid24     -0.3341039298
## NP_006614.to.1layhid24      0.9599440295
## NP_001784.to.1layhid24      0.9223974799
## NP_006092.to.1layhid24     -0.7385900920
## NP_001153651.to.1layhid24   0.6469126667
## NP_001159403.to.1layhid24   0.0004710949
## NP_000116.to.1layhid24     -0.2436906058
## NP_004314.to.1layhid24     -0.3757512019
## NP_060601.to.1layhid24      0.2290743286
## NP_005931.to.1layhid24      2.1428431139
## NP_003003.to.1layhid24     -2.4935007649
## NP_113611.to.1layhid24      0.4456760784
## NP_002002.to.1layhid24     -0.1414654720
## NP_004487.to.1layhid24      0.2089574139
## NP_008950.to.1layhid24     -0.4280712155
## NP_114172.to.1layhid24     -0.1776814216
## NP_001062.to.1layhid24     -0.8666796012
## NP_057547.to.1layhid24      0.2151843602
## NP_054895.to.1layhid24     -0.1063119661
## NP_001246.to.1layhid24      1.1719724463
## NP_036451.to.1layhid24     -0.5676379525
## NP_000624.to.1layhid24      0.7996192093
## NP_001159.to.1layhid24      1.5842189335
## Intercept.to.1layhid25     -0.3925805716
## NP_057427.to.1layhid25     -0.4558335695
## NP_002408.to.1layhid25     -0.8165775016
## NP_000415.to.1layhid25     -0.1285507587
## NP_000413.to.1layhid25     -0.4493290435
## NP_000517.to.1layhid25     -0.4349687401
## NP_004439.to.1layhid25      1.0893616976
## NP_005219.to.1layhid25     -0.7704817598
## NP_058519.to.1layhid25      0.2146534184
## NP_058518.to.1layhid25     -0.0144096215
## NP_001116539.to.1layhid25  -0.0628785135
## NP_061155.to.1layhid25     -0.6019894783
## NP_001035932.to.1layhid25   0.2178527714
## NP_077006.to.1layhid25     -0.9442656563
## NP_000917.to.1layhid25      2.1795811405
## NP_065178.to.1layhid25     -1.8640568367
## NP_006836.to.1layhid25      0.2320963399
## NP_006614.to.1layhid25     -0.6661272101
## NP_001784.to.1layhid25      0.3190644287
## NP_006092.to.1layhid25     -0.6689095293
## NP_001153651.to.1layhid25  -2.0705122462
## NP_001159403.to.1layhid25  -1.0287319932
## NP_000116.to.1layhid25     -0.7222249779
## NP_004314.to.1layhid25      0.6898082217
## NP_060601.to.1layhid25     -2.4236400731
## NP_005931.to.1layhid25     -0.4675875517
## NP_003003.to.1layhid25      1.6012011653
## NP_113611.to.1layhid25      0.7806171337
## NP_002002.to.1layhid25      1.0426157960
## NP_004487.to.1layhid25      0.7948000950
## NP_008950.to.1layhid25      0.5212997642
## NP_114172.to.1layhid25     -1.1823960197
## NP_001062.to.1layhid25     -0.4931362091
## NP_057547.to.1layhid25     -0.4887619144
## NP_054895.to.1layhid25     -0.0462612103
## NP_001246.to.1layhid25     -0.4186061852
## NP_036451.to.1layhid25      1.7608290781
## NP_000624.to.1layhid25     -0.8398761713
## NP_001159.to.1layhid25      0.1157912974
## Intercept.to.1layhid26     -0.4013572279
## NP_057427.to.1layhid26      1.0853383119
## NP_002408.to.1layhid26      0.3651469350
## NP_000415.to.1layhid26      0.0238564951
## NP_000413.to.1layhid26     -1.3809859604
## NP_000517.to.1layhid26     -0.8198301528
## NP_004439.to.1layhid26      0.3573807348
## NP_005219.to.1layhid26     -1.1155656707
## NP_058519.to.1layhid26     -0.0387377828
## NP_058518.to.1layhid26     -0.9101031531
## NP_001116539.to.1layhid26  -1.9708832664
## NP_061155.to.1layhid26      1.9146515499
## NP_001035932.to.1layhid26   0.9509108204
## NP_077006.to.1layhid26     -0.0671190224
## NP_000917.to.1layhid26      2.3448805664
## NP_065178.to.1layhid26      0.3560912327
## NP_006836.to.1layhid26      0.2113794721
## NP_006614.to.1layhid26     -0.2873974360
## NP_001784.to.1layhid26     -1.6921528592
## NP_006092.to.1layhid26     -0.2409736229
## NP_001153651.to.1layhid26   0.1095607380
## NP_001159403.to.1layhid26  -0.4576147214
## NP_000116.to.1layhid26      0.3110950456
## NP_004314.to.1layhid26     -1.4376107950
## NP_060601.to.1layhid26     -0.4891991477
## NP_005931.to.1layhid26     -0.8034238245
## NP_003003.to.1layhid26     -0.7090400169
## NP_113611.to.1layhid26     -0.6955806219
## NP_002002.to.1layhid26      0.2558793564
## NP_004487.to.1layhid26      2.8772287674
## NP_008950.to.1layhid26      0.0237722020
## NP_114172.to.1layhid26     -0.7117620266
## NP_001062.to.1layhid26     -0.6387022080
## NP_057547.to.1layhid26     -0.6852316643
## NP_054895.to.1layhid26     -0.7094945829
## NP_001246.to.1layhid26     -0.7503384347
## NP_036451.to.1layhid26     -2.2505994631
## NP_000624.to.1layhid26      0.6891749545
## NP_001159.to.1layhid26      0.3103406286
## Intercept.to.1layhid27     -0.4583063035
## NP_057427.to.1layhid27      0.1909101900
## NP_002408.to.1layhid27      1.5837881900
## NP_000415.to.1layhid27      0.5118682042
## NP_000413.to.1layhid27      0.2862831937
## NP_000517.to.1layhid27      2.4075970549
## NP_004439.to.1layhid27      1.4683834112
## NP_005219.to.1layhid27     -0.0348004003
## NP_058519.to.1layhid27      2.1256270793
## NP_058518.to.1layhid27      1.1787082252
## NP_001116539.to.1layhid27   0.4595056057
## NP_061155.to.1layhid27     -0.0696999006
## NP_001035932.to.1layhid27  -2.7068126125
## NP_077006.to.1layhid27     -1.2434845253
## NP_000917.to.1layhid27      0.1997271368
## NP_065178.to.1layhid27     -1.1792876532
## NP_006836.to.1layhid27     -0.5581222147
## NP_006614.to.1layhid27     -0.4745879337
## NP_001784.to.1layhid27     -1.5110455948
## NP_006092.to.1layhid27      0.2409973571
## NP_001153651.to.1layhid27   0.1710099882
## NP_001159403.to.1layhid27  -2.4932493094
## NP_000116.to.1layhid27      0.9281226716
## NP_004314.to.1layhid27     -0.6177113441
## NP_060601.to.1layhid27     -1.5403046551
## NP_005931.to.1layhid27      0.9543661536
## NP_003003.to.1layhid27     -0.9722850297
## NP_113611.to.1layhid27     -0.8876753608
## NP_002002.to.1layhid27     -0.6702781969
## NP_004487.to.1layhid27      1.4740047951
## NP_008950.to.1layhid27      1.1304580762
## NP_114172.to.1layhid27     -0.5911974060
## NP_001062.to.1layhid27     -0.6554056652
## NP_057547.to.1layhid27      1.7552020646
## NP_054895.to.1layhid27      1.2479968987
## NP_001246.to.1layhid27      0.4098631352
## NP_036451.to.1layhid27      2.1719693183
## NP_000624.to.1layhid27     -0.2447876404
## NP_001159.to.1layhid27      0.1530413571
## Intercept.to.1layhid28      1.0214074354
## NP_057427.to.1layhid28      1.6490670975
## NP_002408.to.1layhid28     -0.1167026560
## NP_000415.to.1layhid28      1.4668969889
## NP_000413.to.1layhid28      0.1135625505
## NP_000517.to.1layhid28      1.3338029952
## NP_004439.to.1layhid28     -0.3083150280
## NP_005219.to.1layhid28     -0.8205898490
## NP_058519.to.1layhid28     -0.1174123939
## NP_058518.to.1layhid28     -0.0060353447
## NP_001116539.to.1layhid28   0.7135032035
## NP_061155.to.1layhid28      0.2387610511
## NP_001035932.to.1layhid28  -1.0581195593
## NP_077006.to.1layhid28     -0.3562079160
## NP_000917.to.1layhid28      0.4899494883
## NP_065178.to.1layhid28      0.2427525355
## NP_006836.to.1layhid28      1.0795701629
## NP_006614.to.1layhid28      1.0192402407
## NP_001784.to.1layhid28      0.7769902363
## NP_006092.to.1layhid28     -1.2874409484
## NP_001153651.to.1layhid28  -0.5507495815
## NP_001159403.to.1layhid28   0.5200652820
## NP_000116.to.1layhid28      0.6764325761
## NP_004314.to.1layhid28      0.9204333291
## NP_060601.to.1layhid28     -2.2544334740
## NP_005931.to.1layhid28      1.6002454170
## NP_003003.to.1layhid28     -0.1339695558
## NP_113611.to.1layhid28      1.8757069321
## NP_002002.to.1layhid28      2.2387668074
## NP_004487.to.1layhid28     -0.1925509832
## NP_008950.to.1layhid28     -1.6791673560
## NP_114172.to.1layhid28      1.7817445267
## NP_001062.to.1layhid28      1.9251239921
## NP_057547.to.1layhid28      1.4719871206
## NP_054895.to.1layhid28      0.3453790477
## NP_001246.to.1layhid28      1.3573367394
## NP_036451.to.1layhid28     -0.4383797927
## NP_000624.to.1layhid28     -0.7516422828
## NP_001159.to.1layhid28     -0.4387488475
## Intercept.to.1layhid29     -1.4570793034
## NP_057427.to.1layhid29      0.1663336621
## NP_002408.to.1layhid29     -0.4356028355
## NP_000415.to.1layhid29      0.7667902581
## NP_000413.to.1layhid29     -0.3792007028
## NP_000517.to.1layhid29     -0.0894473803
## NP_004439.to.1layhid29      0.3458832152
## NP_005219.to.1layhid29     -0.9247115661
## NP_058519.to.1layhid29     -0.5625166467
## NP_058518.to.1layhid29      1.1337292109
## NP_001116539.to.1layhid29   0.1628541388
## NP_061155.to.1layhid29     -0.5474412296
## NP_001035932.to.1layhid29  -1.2522502746
## NP_077006.to.1layhid29      2.7513767349
## NP_000917.to.1layhid29     -0.9203176490
## NP_065178.to.1layhid29      0.5945837107
## NP_006836.to.1layhid29      2.5331461154
## NP_006614.to.1layhid29     -0.2168700895
## NP_001784.to.1layhid29     -0.2648310831
## NP_006092.to.1layhid29      0.4240726931
## NP_001153651.to.1layhid29  -0.3107370345
## NP_001159403.to.1layhid29   1.8380849549
## NP_000116.to.1layhid29     -1.1536573596
## NP_004314.to.1layhid29      0.8118402074
## NP_060601.to.1layhid29      0.6110842440
## NP_005931.to.1layhid29     -1.0203482038
## NP_003003.to.1layhid29     -3.2064948334
## NP_113611.to.1layhid29     -1.3184995402
## NP_002002.to.1layhid29     -1.3758411791
## NP_004487.to.1layhid29     -0.2387244625
## NP_008950.to.1layhid29     -0.7025930082
## NP_114172.to.1layhid29      0.5880743920
## NP_001062.to.1layhid29      0.6042302783
## NP_057547.to.1layhid29     -2.0815157158
## NP_054895.to.1layhid29     -0.3271027076
## NP_001246.to.1layhid29      0.7344603315
## NP_036451.to.1layhid29     -1.4453703582
## NP_000624.to.1layhid29      1.2258857577
## NP_001159.to.1layhid29      0.9651388939
## Intercept.to.1layhid30     -0.7817245948
## NP_057427.to.1layhid30     -0.0144080706
## NP_002408.to.1layhid30      0.2547339386
## NP_000415.to.1layhid30     -1.0455804366
## NP_000413.to.1layhid30     -1.7997889225
## NP_000517.to.1layhid30     -0.1976476660
## NP_004439.to.1layhid30     -0.2411605778
## NP_005219.to.1layhid30     -0.7586311803
## NP_058519.to.1layhid30     -0.2497437592
## NP_058518.to.1layhid30      0.9534941475
## NP_001116539.to.1layhid30   0.0164060174
## NP_061155.to.1layhid30      0.3122584436
## NP_001035932.to.1layhid30  -0.1995486025
## NP_077006.to.1layhid30      0.3790504128
## NP_000917.to.1layhid30      2.2128326285
## NP_065178.to.1layhid30     -0.7121636043
## NP_006836.to.1layhid30     -0.1400909159
## NP_006614.to.1layhid30     -1.4644686487
## NP_001784.to.1layhid30      0.1378078831
## NP_006092.to.1layhid30      0.7534873089
## NP_001153651.to.1layhid30  -0.4246002563
## NP_001159403.to.1layhid30  -1.2695801588
## NP_000116.to.1layhid30      0.2297873326
## NP_004314.to.1layhid30      0.7821603560
## NP_060601.to.1layhid30     -1.5775298172
## NP_005931.to.1layhid30      1.2477879967
## NP_003003.to.1layhid30     -1.6178951941
## NP_113611.to.1layhid30     -0.9169341418
## NP_002002.to.1layhid30     -1.4323459064
## NP_004487.to.1layhid30      1.0613563073
## NP_008950.to.1layhid30      1.8082348176
## NP_114172.to.1layhid30      1.0365737018
## NP_001062.to.1layhid30     -1.8684479775
## NP_057547.to.1layhid30     -0.7677989213
## NP_054895.to.1layhid30      1.1015351375
## NP_001246.to.1layhid30      1.8615832000
## NP_036451.to.1layhid30     -1.9231373805
## NP_000624.to.1layhid30     -0.0298951981
## NP_001159.to.1layhid30      0.0794171919
## Intercept.to.2layhid1      -0.9588090578
## 1layhid1.to.2layhid1        0.3587857443
## 1layhid2.to.2layhid1        0.0215476877
## 1layhid3.to.2layhid1       -1.3524427366
## 1layhid4.to.2layhid1        0.0821795320
## 1layhid5.to.2layhid1       -0.0755256598
## 1layhid6.to.2layhid1       -0.2971937178
## 1layhid7.to.2layhid1        0.2599763620
## 1layhid8.to.2layhid1       -1.8518798978
## 1layhid9.to.2layhid1       -1.1802990760
## 1layhid10.to.2layhid1      -1.3144531944
## 1layhid11.to.2layhid1      -1.6663993951
## 1layhid12.to.2layhid1      -0.8693489158
## 1layhid13.to.2layhid1      -3.8496641741
## 1layhid14.to.2layhid1       0.6405436361
## 1layhid15.to.2layhid1      -2.8086813317
## 1layhid16.to.2layhid1       1.3436588033
## 1layhid17.to.2layhid1       2.1507674913
## 1layhid18.to.2layhid1      -1.3826315757
## 1layhid19.to.2layhid1      -2.1166236003
## 1layhid20.to.2layhid1       2.4739151856
## 1layhid21.to.2layhid1       1.1170405247
## 1layhid22.to.2layhid1       0.0159083431
## 1layhid23.to.2layhid1       1.4110241172
## 1layhid24.to.2layhid1       1.2221857687
## 1layhid25.to.2layhid1       2.6418779205
## 1layhid26.to.2layhid1      -0.5663042390
## 1layhid27.to.2layhid1      -0.1033316430
## 1layhid28.to.2layhid1       0.5031498882
## 1layhid29.to.2layhid1      -0.3691246105
## 1layhid30.to.2layhid1       0.8209893237
## Intercept.to.2layhid2       0.3725006393
## 1layhid1.to.2layhid2       -0.2987003384
## 1layhid2.to.2layhid2        0.3432146041
## 1layhid3.to.2layhid2        2.1140080038
## 1layhid4.to.2layhid2       -1.5902466013
## 1layhid5.to.2layhid2       -0.1769444645
## 1layhid6.to.2layhid2       -0.1289265241
## 1layhid7.to.2layhid2        0.2333425210
## 1layhid8.to.2layhid2       -0.1122149267
## 1layhid9.to.2layhid2       -0.2372175506
## 1layhid10.to.2layhid2      -0.7626994091
## 1layhid11.to.2layhid2      -0.2421914887
## 1layhid12.to.2layhid2       0.4494337525
## 1layhid13.to.2layhid2      -0.3108518475
## 1layhid14.to.2layhid2      -0.0367336703
## 1layhid15.to.2layhid2       0.3113770458
## 1layhid16.to.2layhid2      -0.1008533567
## 1layhid17.to.2layhid2       1.8807889330
## 1layhid18.to.2layhid2       0.5487802786
## 1layhid19.to.2layhid2      -0.1640828901
## 1layhid20.to.2layhid2      -0.5748064849
## 1layhid21.to.2layhid2      -0.8977714028
## 1layhid22.to.2layhid2      -0.1555421186
## 1layhid23.to.2layhid2      -2.0517263227
## 1layhid24.to.2layhid2       0.7776167078
## 1layhid25.to.2layhid2      -0.5940849036
## 1layhid26.to.2layhid2       0.5417029057
## 1layhid27.to.2layhid2      -1.6006590178
## 1layhid28.to.2layhid2      -1.8001516065
## 1layhid29.to.2layhid2       3.6074293073
## 1layhid30.to.2layhid2       0.3142626860
## Intercept.to.2layhid3      -0.3138774355
## 1layhid1.to.2layhid3        0.1500662097
## 1layhid2.to.2layhid3        0.7842121300
## 1layhid3.to.2layhid3       -1.4242878042
## 1layhid4.to.2layhid3        1.6174713947
## 1layhid5.to.2layhid3        0.3803475482
## 1layhid6.to.2layhid3        0.6371835633
## 1layhid7.to.2layhid3        2.0223414734
## 1layhid8.to.2layhid3        0.3609824832
## 1layhid9.to.2layhid3       -2.1484912414
## 1layhid10.to.2layhid3      -0.2982550605
## 1layhid11.to.2layhid3       0.6552597616
## 1layhid12.to.2layhid3       1.6008592446
## 1layhid13.to.2layhid3      -2.7129916364
## 1layhid14.to.2layhid3      -0.8029337020
## 1layhid15.to.2layhid3      -1.6711940996
## 1layhid16.to.2layhid3      -0.1496516385
## 1layhid17.to.2layhid3       2.6944073770
## 1layhid18.to.2layhid3      -1.4740584247
## 1layhid19.to.2layhid3      -0.7696103742
## 1layhid20.to.2layhid3       1.0514442833
## 1layhid21.to.2layhid3      -0.8407239359
## 1layhid22.to.2layhid3       0.7747812448
## 1layhid23.to.2layhid3      -0.6831518173
## 1layhid24.to.2layhid3      -0.2532060686
## 1layhid25.to.2layhid3      -0.0629133012
## 1layhid26.to.2layhid3      -0.4755392531
## 1layhid27.to.2layhid3       2.0579388072
## 1layhid28.to.2layhid3       0.1789424418
## 1layhid29.to.2layhid3      -0.6872164068
## 1layhid30.to.2layhid3       0.0109857197
## Intercept.to.2layhid4      -0.4674887767
## 1layhid1.to.2layhid4        1.0723967472
## 1layhid2.to.2layhid4       -0.1321770716
## 1layhid3.to.2layhid4       -0.1659826324
## 1layhid4.to.2layhid4        1.3795004834
## 1layhid5.to.2layhid4        0.9664358590
## 1layhid6.to.2layhid4       -0.4906952056
## 1layhid7.to.2layhid4        0.0442877415
## 1layhid8.to.2layhid4        0.5784572573
## 1layhid9.to.2layhid4       -0.9315374811
## 1layhid10.to.2layhid4       0.3611554279
## 1layhid11.to.2layhid4      -0.7170356157
## 1layhid12.to.2layhid4       0.3053849926
## 1layhid13.to.2layhid4      -0.5522973428
## 1layhid14.to.2layhid4       0.4519445562
## 1layhid15.to.2layhid4      -1.5254014807
## 1layhid16.to.2layhid4      -0.2089425939
## 1layhid17.to.2layhid4      -0.9925565230
## 1layhid18.to.2layhid4      -0.2655916142
## 1layhid19.to.2layhid4       1.1135565472
## 1layhid20.to.2layhid4       1.9373077764
## 1layhid21.to.2layhid4       0.7940784037
## 1layhid22.to.2layhid4      -0.1428730262
## 1layhid23.to.2layhid4      -0.6411943241
## 1layhid24.to.2layhid4       0.5548511765
## 1layhid25.to.2layhid4       0.3229018602
## 1layhid26.to.2layhid4      -0.2582752309
## 1layhid27.to.2layhid4      -0.6171844375
## 1layhid28.to.2layhid4       0.4741931379
## 1layhid29.to.2layhid4      -0.3119893288
## 1layhid30.to.2layhid4      -0.1350445148
## Intercept.to.2layhid5      -0.4736692442
## 1layhid1.to.2layhid5       -0.4697377189
## 1layhid2.to.2layhid5       -0.1931556908
## 1layhid3.to.2layhid5        0.7766428577
## 1layhid4.to.2layhid5       -1.7356448284
## 1layhid5.to.2layhid5        0.7195547383
## 1layhid6.to.2layhid5        1.5775581263
## 1layhid7.to.2layhid5       -1.9353962567
## 1layhid8.to.2layhid5       -0.3191611673
## 1layhid9.to.2layhid5        0.4760907323
## 1layhid10.to.2layhid5      -0.9958927986
## 1layhid11.to.2layhid5       0.8444838001
## 1layhid12.to.2layhid5       1.7920378672
## 1layhid13.to.2layhid5       1.7445986306
## 1layhid14.to.2layhid5       2.0476228757
## 1layhid15.to.2layhid5       1.7412234572
## 1layhid16.to.2layhid5       0.3662063905
## 1layhid17.to.2layhid5       0.3157510181
## 1layhid18.to.2layhid5       0.1908115671
## 1layhid19.to.2layhid5       0.4162043612
## 1layhid20.to.2layhid5      -0.6202948239
## 1layhid21.to.2layhid5      -1.1912444905
## 1layhid22.to.2layhid5      -1.0358891244
## 1layhid23.to.2layhid5      -0.2926623679
## 1layhid24.to.2layhid5      -0.8380240756
## 1layhid25.to.2layhid5      -0.2594192876
## 1layhid26.to.2layhid5      -1.4825323199
## 1layhid27.to.2layhid5      -0.6375416895
## 1layhid28.to.2layhid5       0.2704731265
## 1layhid29.to.2layhid5       1.4178556341
## 1layhid30.to.2layhid5      -0.3874765326
## Intercept.to.2layhid6       0.0012264379
## 1layhid1.to.2layhid6        1.5356072441
## 1layhid2.to.2layhid6        1.4143174744
## 1layhid3.to.2layhid6        0.2423283824
## 1layhid4.to.2layhid6        0.7472252740
## 1layhid5.to.2layhid6       -0.5876388740
## 1layhid6.to.2layhid6        1.2898138552
## 1layhid7.to.2layhid6        1.6780572881
## 1layhid8.to.2layhid6        3.1582044018
## 1layhid9.to.2layhid6       -0.6375718557
## 1layhid10.to.2layhid6       1.2901955469
## 1layhid11.to.2layhid6      -0.9834681642
## 1layhid12.to.2layhid6       0.9674704030
## 1layhid13.to.2layhid6      -0.4659086832
## 1layhid14.to.2layhid6      -0.7675717310
## 1layhid15.to.2layhid6       1.6809282503
## 1layhid16.to.2layhid6      -0.5711287144
## 1layhid17.to.2layhid6       0.6875258080
## 1layhid18.to.2layhid6      -0.2590964310
## 1layhid19.to.2layhid6       0.5038396089
## 1layhid20.to.2layhid6      -0.9064253272
## 1layhid21.to.2layhid6       1.1097763708
## 1layhid22.to.2layhid6       0.5434647413
## 1layhid23.to.2layhid6       0.1745394012
## 1layhid24.to.2layhid6      -0.9503939768
## 1layhid25.to.2layhid6       0.2156692761
## 1layhid26.to.2layhid6       1.6389293797
## 1layhid27.to.2layhid6       1.0693278378
## 1layhid28.to.2layhid6      -0.7171366431
## 1layhid29.to.2layhid6       1.8425749003
## 1layhid30.to.2layhid6       0.1152246113
## Intercept.to.2layhid7       0.3896045256
## 1layhid1.to.2layhid7       -1.8420156937
## 1layhid2.to.2layhid7        0.5659866406
## 1layhid3.to.2layhid7        0.8682128486
## 1layhid4.to.2layhid7       -0.0410008658
## 1layhid5.to.2layhid7        1.1673611589
## 1layhid6.to.2layhid7       -0.5808468916
## 1layhid7.to.2layhid7       -1.2361949463
## 1layhid8.to.2layhid7       -1.4139691710
## 1layhid9.to.2layhid7       -2.1052471880
## 1layhid10.to.2layhid7      -1.5855940142
## 1layhid11.to.2layhid7       0.1167414872
## 1layhid12.to.2layhid7      -0.2579215397
## 1layhid13.to.2layhid7      -3.8629599161
## 1layhid14.to.2layhid7       2.9082216330
## 1layhid15.to.2layhid7      -2.6634033268
## 1layhid16.to.2layhid7      -0.1090217956
## 1layhid17.to.2layhid7       1.3724411488
## 1layhid18.to.2layhid7       0.4038063743
## 1layhid19.to.2layhid7      -0.8274156639
## 1layhid20.to.2layhid7       3.6730510054
## 1layhid21.to.2layhid7      -0.1515616553
## 1layhid22.to.2layhid7      -1.8866050439
## 1layhid23.to.2layhid7       0.6042166271
## 1layhid24.to.2layhid7      -0.0597108926
## 1layhid25.to.2layhid7       0.3795961052
## 1layhid26.to.2layhid7      -1.6875295953
## 1layhid27.to.2layhid7      -2.5506539082
## 1layhid28.to.2layhid7      -0.8911115411
## 1layhid29.to.2layhid7       0.3678378263
## 1layhid30.to.2layhid7      -0.5063546010
## Intercept.to.2layhid8      -0.6841589824
## 1layhid1.to.2layhid8       -1.3897993361
## 1layhid2.to.2layhid8       -1.4922060454
## 1layhid3.to.2layhid8       -4.0226708541
## 1layhid4.to.2layhid8       -0.3843197888
## 1layhid5.to.2layhid8        0.0664977915
## 1layhid6.to.2layhid8       -0.0620718634
## 1layhid7.to.2layhid8       -0.2200860427
## 1layhid8.to.2layhid8        0.8630924974
## 1layhid9.to.2layhid8        2.3433228498
## 1layhid10.to.2layhid8       0.8150835676
## 1layhid11.to.2layhid8      -0.2956758276
## 1layhid12.to.2layhid8       1.2843989293
## 1layhid13.to.2layhid8       0.0516546955
## 1layhid14.to.2layhid8       1.7763954559
## 1layhid15.to.2layhid8       2.3760459704
## 1layhid16.to.2layhid8      -0.9577932035
## 1layhid17.to.2layhid8       0.7184100212
## 1layhid18.to.2layhid8       1.0264037733
## 1layhid19.to.2layhid8       0.0551849119
## 1layhid20.to.2layhid8       2.1767911892
## 1layhid21.to.2layhid8      -1.0947738371
## 1layhid22.to.2layhid8      -0.1267239449
## 1layhid23.to.2layhid8      -1.5894301964
## 1layhid24.to.2layhid8      -0.0941246220
## 1layhid25.to.2layhid8       0.6127924368
## 1layhid26.to.2layhid8      -0.7069865700
## 1layhid27.to.2layhid8      -0.6391925545
## 1layhid28.to.2layhid8       1.5331281378
## 1layhid29.to.2layhid8      -0.7276305794
## 1layhid30.to.2layhid8       1.0084194362
## Intercept.to.2layhid9      -0.6586981998
## 1layhid1.to.2layhid9       -0.4674067714
## 1layhid2.to.2layhid9        0.3507950838
## 1layhid3.to.2layhid9       -1.1671174548
## 1layhid4.to.2layhid9        0.1259993012
## 1layhid5.to.2layhid9        4.6464357471
## 1layhid6.to.2layhid9        1.0103362052
## 1layhid7.to.2layhid9       -1.7215841149
## 1layhid8.to.2layhid9        0.1962623561
## 1layhid9.to.2layhid9       -0.8333663402
## 1layhid10.to.2layhid9      -0.5435794964
## 1layhid11.to.2layhid9      -0.4417782383
## 1layhid12.to.2layhid9       0.2990071083
## 1layhid13.to.2layhid9      -0.7328306065
## 1layhid14.to.2layhid9       0.6760060044
## 1layhid15.to.2layhid9       0.2233227369
## 1layhid16.to.2layhid9       0.5858925133
## 1layhid17.to.2layhid9      -0.7194695400
## 1layhid18.to.2layhid9      -1.0876136109
## 1layhid19.to.2layhid9       3.0553704328
## 1layhid20.to.2layhid9       1.1534130668
## 1layhid21.to.2layhid9       1.1291577058
## 1layhid22.to.2layhid9       0.4068259766
## 1layhid23.to.2layhid9       1.2337174447
## 1layhid24.to.2layhid9      -0.5673426783
## 1layhid25.to.2layhid9       2.3258702026
## 1layhid26.to.2layhid9       1.5655148321
## 1layhid27.to.2layhid9      -1.7968749685
## 1layhid28.to.2layhid9      -0.4717133863
## 1layhid29.to.2layhid9       0.9562778922
## 1layhid30.to.2layhid9       1.2152273327
## Intercept.to.2layhid10     -0.1868550432
## 1layhid1.to.2layhid10      -0.3183602980
## 1layhid2.to.2layhid10       1.1901276085
## 1layhid3.to.2layhid10       1.8204237772
## 1layhid4.to.2layhid10      -0.1377436387
## 1layhid5.to.2layhid10      -2.2306733718
## 1layhid6.to.2layhid10      -0.0692883607
## 1layhid7.to.2layhid10       0.5575984941
## 1layhid8.to.2layhid10      -0.0021676384
## 1layhid9.to.2layhid10      -1.5843570240
## 1layhid10.to.2layhid10      0.3080964205
## 1layhid11.to.2layhid10     -0.9890322060
## 1layhid12.to.2layhid10      0.3965966612
## 1layhid13.to.2layhid10      0.5843970634
## 1layhid14.to.2layhid10     -0.7159373449
## 1layhid15.to.2layhid10      1.6820835405
## 1layhid16.to.2layhid10      0.4523201437
## 1layhid17.to.2layhid10      0.6908967669
## 1layhid18.to.2layhid10     -1.3619608201
## 1layhid19.to.2layhid10      0.3023870166
## 1layhid20.to.2layhid10      0.4805871922
## 1layhid21.to.2layhid10     -0.6697948355
## 1layhid22.to.2layhid10     -2.0739667155
## 1layhid23.to.2layhid10      1.0948605267
## 1layhid24.to.2layhid10      1.0510346120
## 1layhid25.to.2layhid10     -0.3962882998
## 1layhid26.to.2layhid10      2.0354809951
## 1layhid27.to.2layhid10     -2.2442934980
## 1layhid28.to.2layhid10     -2.4497087420
## 1layhid29.to.2layhid10      0.1893775175
## 1layhid30.to.2layhid10     -0.5227421252
## Intercept.to.2layhid11     -1.7121181870
## 1layhid1.to.2layhid11      -0.0540461442
## 1layhid2.to.2layhid11       0.1111736056
## 1layhid3.to.2layhid11       1.0966813958
## 1layhid4.to.2layhid11      -1.1128497629
## 1layhid5.to.2layhid11      -0.1137135110
## 1layhid6.to.2layhid11       1.3532095527
## 1layhid7.to.2layhid11      -0.2606613815
## 1layhid8.to.2layhid11      -0.8647896803
## 1layhid9.to.2layhid11       0.1902796949
## 1layhid10.to.2layhid11     -2.4521557322
## 1layhid11.to.2layhid11     -1.0830256793
## 1layhid12.to.2layhid11      2.7015589208
## 1layhid13.to.2layhid11      0.9163501765
## 1layhid14.to.2layhid11      0.5974416915
## 1layhid15.to.2layhid11      1.6374399897
## 1layhid16.to.2layhid11      1.8027422898
## 1layhid17.to.2layhid11      0.8788199014
## 1layhid18.to.2layhid11      1.5415255405
## 1layhid19.to.2layhid11     -2.7447541088
## 1layhid20.to.2layhid11      0.0305673603
## 1layhid21.to.2layhid11     -1.8370972787
## 1layhid22.to.2layhid11     -1.2110314888
## 1layhid23.to.2layhid11      2.5458720414
## 1layhid24.to.2layhid11      0.5196666295
## 1layhid25.to.2layhid11      0.6262919548
## 1layhid26.to.2layhid11     -0.3504171731
## 1layhid27.to.2layhid11     -2.5989216481
## 1layhid28.to.2layhid11      1.8162006167
## 1layhid29.to.2layhid11      1.7050973714
## 1layhid30.to.2layhid11     -1.5396470479
## Intercept.to.2layhid12     -0.8309964701
## 1layhid1.to.2layhid12      -0.3349769305
## 1layhid2.to.2layhid12      -0.7005881450
## 1layhid3.to.2layhid12       2.1097001893
## 1layhid4.to.2layhid12      -0.6169404641
## 1layhid5.to.2layhid12      -1.3500608150
## 1layhid6.to.2layhid12      -0.7140780039
## 1layhid7.to.2layhid12      -0.8862448619
## 1layhid8.to.2layhid12       0.0492583705
## 1layhid9.to.2layhid12      -0.1659486336
## 1layhid10.to.2layhid12      0.9800495144
## 1layhid11.to.2layhid12      0.6434004474
## 1layhid12.to.2layhid12     -0.4463066555
## 1layhid13.to.2layhid12     -0.3565343095
## 1layhid14.to.2layhid12     -1.9815141234
## 1layhid15.to.2layhid12      1.1231298368
## 1layhid16.to.2layhid12      0.2637766417
## 1layhid17.to.2layhid12      0.6799649898
## 1layhid18.to.2layhid12     -0.4451283895
## 1layhid19.to.2layhid12      0.7727739825
## 1layhid20.to.2layhid12     -2.2805978101
## 1layhid21.to.2layhid12     -1.3345243672
## 1layhid22.to.2layhid12     -1.8049306402
## 1layhid23.to.2layhid12     -1.8444208378
## 1layhid24.to.2layhid12      0.0969444329
## 1layhid25.to.2layhid12     -1.1019155302
## 1layhid26.to.2layhid12      1.4290914580
## 1layhid27.to.2layhid12     -0.5724523405
## 1layhid28.to.2layhid12      1.4538713205
## 1layhid29.to.2layhid12     -0.9697919149
## 1layhid30.to.2layhid12     -0.3256961421
## Intercept.to.2layhid13     -0.4266838100
## 1layhid1.to.2layhid13      -2.5884410770
## 1layhid2.to.2layhid13       1.2140659662
## 1layhid3.to.2layhid13      -0.4511853209
## 1layhid4.to.2layhid13       1.0026185556
## 1layhid5.to.2layhid13       3.0392780340
## 1layhid6.to.2layhid13      -0.7875164308
## 1layhid7.to.2layhid13      -0.0659479012
## 1layhid8.to.2layhid13       1.8533730961
## 1layhid9.to.2layhid13       1.5000081915
## 1layhid10.to.2layhid13      1.3355840409
## 1layhid11.to.2layhid13      0.8515537465
## 1layhid12.to.2layhid13     -0.9827438701
## 1layhid13.to.2layhid13     -1.4893067463
## 1layhid14.to.2layhid13      0.4175425821
## 1layhid15.to.2layhid13     -0.1447721109
## 1layhid16.to.2layhid13     -1.7780584077
## 1layhid17.to.2layhid13      0.4394722043
## 1layhid18.to.2layhid13     -1.6372109740
## 1layhid19.to.2layhid13      1.0113250087
## 1layhid20.to.2layhid13     -0.1211779910
## 1layhid21.to.2layhid13      2.2587444423
## 1layhid22.to.2layhid13     -1.3515033299
## 1layhid23.to.2layhid13      1.8999089062
## 1layhid24.to.2layhid13      0.8282503848
## 1layhid25.to.2layhid13      0.6333020700
## 1layhid26.to.2layhid13      0.9135553506
## 1layhid27.to.2layhid13      1.5139278739
## 1layhid28.to.2layhid13      1.5941899383
## 1layhid29.to.2layhid13     -0.1302505437
## 1layhid30.to.2layhid13     -1.4004008075
## Intercept.to.2layhid14     -2.1509671960
## 1layhid1.to.2layhid14       1.9678417163
## 1layhid2.to.2layhid14       1.6408251909
## 1layhid3.to.2layhid14       2.9129991278
## 1layhid4.to.2layhid14       2.8326259449
## 1layhid5.to.2layhid14      -1.1811559315
## 1layhid6.to.2layhid14       0.6484642051
## 1layhid7.to.2layhid14       1.9261725732
## 1layhid8.to.2layhid14      -0.4397788107
## 1layhid9.to.2layhid14      -2.1777348421
## 1layhid10.to.2layhid14     -0.1770334650
## 1layhid11.to.2layhid14     -0.3182637280
## 1layhid12.to.2layhid14      0.1949441595
## 1layhid13.to.2layhid14      0.7203934184
## 1layhid14.to.2layhid14     -1.3806182684
## 1layhid15.to.2layhid14      2.0853328442
## 1layhid16.to.2layhid14      0.2848507958
## 1layhid17.to.2layhid14      1.2244935734
## 1layhid18.to.2layhid14     -0.6292825813
## 1layhid19.to.2layhid14     -0.7191142012
## 1layhid20.to.2layhid14     -0.0718670723
## 1layhid21.to.2layhid14     -0.1521584832
## 1layhid22.to.2layhid14      0.9924188606
## 1layhid23.to.2layhid14      0.4166385613
## 1layhid24.to.2layhid14      0.0490495756
## 1layhid25.to.2layhid14      0.1915785395
## 1layhid26.to.2layhid14      1.2367037020
## 1layhid27.to.2layhid14      0.9896371489
## 1layhid28.to.2layhid14     -0.6735674572
## 1layhid29.to.2layhid14      2.4913338784
## 1layhid30.to.2layhid14      2.8776031261
## Intercept.to.2layhid15      1.1267832793
## 1layhid1.to.2layhid15      -3.5247407168
## 1layhid2.to.2layhid15      -3.6161801237
## 1layhid3.to.2layhid15      -3.9680340859
## 1layhid4.to.2layhid15       1.0580259311
## 1layhid5.to.2layhid15       0.7226695311
## 1layhid6.to.2layhid15      -1.6035233385
## 1layhid7.to.2layhid15      -1.8046213887
## 1layhid8.to.2layhid15      -3.3859211179
## 1layhid9.to.2layhid15       1.6819011087
## 1layhid10.to.2layhid15      0.0005115041
## 1layhid11.to.2layhid15      0.5953184067
## 1layhid12.to.2layhid15     -2.0372133266
## 1layhid13.to.2layhid15      1.6522059316
## 1layhid14.to.2layhid15      2.0991154296
## 1layhid15.to.2layhid15     -0.3049962609
## 1layhid16.to.2layhid15      1.5557308311
## 1layhid17.to.2layhid15     -2.7925798603
## 1layhid18.to.2layhid15      0.4172293900
## 1layhid19.to.2layhid15     -3.4187257911
## 1layhid20.to.2layhid15     -0.2498966030
## 1layhid21.to.2layhid15      1.0918073925
## 1layhid22.to.2layhid15     -3.1095116276
## 1layhid23.to.2layhid15      0.4980978724
## 1layhid24.to.2layhid15     -0.8318892217
## 1layhid25.to.2layhid15     -0.3736104007
## 1layhid26.to.2layhid15     -0.7365428019
## 1layhid27.to.2layhid15     -2.8765328684
## 1layhid28.to.2layhid15      0.6211990507
## 1layhid29.to.2layhid15     -1.3403744011
## 1layhid30.to.2layhid15     -3.5547254677
## Intercept.to.3layhid1       0.3138497319
## 2layhid1.to.3layhid1        1.6091431811
## 2layhid2.to.3layhid1        0.4006491310
## 2layhid3.to.3layhid1       -0.7548238959
## 2layhid4.to.3layhid1        1.8979766976
## 2layhid5.to.3layhid1       -0.2765653234
## 2layhid6.to.3layhid1       -0.9845531169
## 2layhid7.to.3layhid1        2.7116781923
## 2layhid8.to.3layhid1        0.1427778025
## 2layhid9.to.3layhid1       -0.5300597961
## 2layhid10.to.3layhid1       0.5833559142
## 2layhid11.to.3layhid1       2.0236415447
## 2layhid12.to.3layhid1       1.3389450645
## 2layhid13.to.3layhid1      -1.2740125297
## 2layhid14.to.3layhid1       0.1556482971
## 2layhid15.to.3layhid1       1.6044117701
## Intercept.to.3layhid2      -0.2867930399
## 2layhid1.to.3layhid2        3.1942967643
## 2layhid2.to.3layhid2        0.3456330894
## 2layhid3.to.3layhid2        1.6857573597
## 2layhid4.to.3layhid2        0.2963943579
## 2layhid5.to.3layhid2       -0.9328625469
## 2layhid6.to.3layhid2       -2.8173774656
## 2layhid7.to.3layhid2        1.7281310369
## 2layhid8.to.3layhid2       -0.0752937915
## 2layhid9.to.3layhid2        1.5828190080
## 2layhid10.to.3layhid2      -2.6931643756
## 2layhid11.to.3layhid2       1.8708310664
## 2layhid12.to.3layhid2      -0.6333260329
## 2layhid13.to.3layhid2       0.1899151085
## 2layhid14.to.3layhid2      -0.9330077901
## 2layhid15.to.3layhid2       0.1989786442
## Intercept.to.3layhid3       1.6972115446
## 2layhid1.to.3layhid3       -4.3479427537
## 2layhid2.to.3layhid3       -0.1387938458
## 2layhid3.to.3layhid3       -0.7899488744
## 2layhid4.to.3layhid3       -0.3215547038
## 2layhid5.to.3layhid3       -0.3787448512
## 2layhid6.to.3layhid3        0.2007692360
## 2layhid7.to.3layhid3       -2.6376489872
## 2layhid8.to.3layhid3        0.9949794274
## 2layhid9.to.3layhid3        0.5206611987
## 2layhid10.to.3layhid3      -0.6052685254
## 2layhid11.to.3layhid3      -0.0887918700
## 2layhid12.to.3layhid3       1.7821348677
## 2layhid13.to.3layhid3       0.5719441232
## 2layhid14.to.3layhid3       0.9247146654
## 2layhid15.to.3layhid3      -0.5230178907
## Intercept.to.3layhid4       0.8237907369
## 2layhid1.to.3layhid4        0.2650124522
## 2layhid2.to.3layhid4       -0.4943364876
## 2layhid3.to.3layhid4       -0.0687789697
## 2layhid4.to.3layhid4       -0.3692369680
## 2layhid5.to.3layhid4       -3.2060191946
## 2layhid6.to.3layhid4        2.7427194962
## 2layhid7.to.3layhid4       -1.0155803067
## 2layhid8.to.3layhid4       -0.1629441424
## 2layhid9.to.3layhid4        0.0367172266
## 2layhid10.to.3layhid4      -1.8341853396
## 2layhid11.to.3layhid4      -3.1404285011
## 2layhid12.to.3layhid4      -0.8601623457
## 2layhid13.to.3layhid4       1.5939662311
## 2layhid14.to.3layhid4      -0.0533595947
## 2layhid15.to.3layhid4      -0.7520745010
## Intercept.to.3layhid5      -0.6816659730
## 2layhid1.to.3layhid5       -2.4978788802
## 2layhid2.to.3layhid5        1.2987489024
## 2layhid3.to.3layhid5       -1.1833326198
## 2layhid4.to.3layhid5       -0.0589129571
## 2layhid5.to.3layhid5        2.1079167413
## 2layhid6.to.3layhid5        0.4127624705
## 2layhid7.to.3layhid5       -1.1816337309
## 2layhid8.to.3layhid5       -0.2070762422
## 2layhid9.to.3layhid5       -0.4279441552
## 2layhid10.to.3layhid5       0.2767421280
## 2layhid11.to.3layhid5       1.3989122543
## 2layhid12.to.3layhid5       3.5175305759
## 2layhid13.to.3layhid5      -1.4271263470
## 2layhid14.to.3layhid5      -0.3000611785
## 2layhid15.to.3layhid5      -1.1477645007
## Intercept.to.3layhid6       0.4858980551
## 2layhid1.to.3layhid6        0.7903727685
## 2layhid2.to.3layhid6       -2.8382243436
## 2layhid3.to.3layhid6       -0.4698918439
## 2layhid4.to.3layhid6        1.7084697110
## 2layhid5.to.3layhid6       -0.1557039152
## 2layhid6.to.3layhid6       -0.1520831725
## 2layhid7.to.3layhid6       -0.4438442614
## 2layhid8.to.3layhid6        2.9678121974
## 2layhid9.to.3layhid6        0.9696607342
## 2layhid10.to.3layhid6      -1.7385194814
## 2layhid11.to.3layhid6      -2.2500149217
## 2layhid12.to.3layhid6      -0.6399898880
## 2layhid13.to.3layhid6       1.0915766803
## 2layhid14.to.3layhid6      -0.5268682980
## 2layhid15.to.3layhid6       1.6075077145
## Intercept.to.3layhid7      -0.2563902337
## 2layhid1.to.3layhid7       -1.0086164217
## 2layhid2.to.3layhid7        1.0985727318
## 2layhid3.to.3layhid7       -0.3180889727
## 2layhid4.to.3layhid7        1.6721076052
## 2layhid5.to.3layhid7        0.1357547865
## 2layhid6.to.3layhid7        1.2756805097
## 2layhid7.to.3layhid7       -2.4541073034
## 2layhid8.to.3layhid7       -0.2188723500
## 2layhid9.to.3layhid7        1.2359589506
## 2layhid10.to.3layhid7      -1.1980517582
## 2layhid11.to.3layhid7      -0.4979963347
## 2layhid12.to.3layhid7      -1.3829366288
## 2layhid13.to.3layhid7      -0.0214527453
## 2layhid14.to.3layhid7       1.6849483588
## 2layhid15.to.3layhid7      -3.3918463284
## Intercept.to.3layhid8      -1.0689751863
## 2layhid1.to.3layhid8       -1.6871798284
## 2layhid2.to.3layhid8        0.3687128432
## 2layhid3.to.3layhid8       -2.4189061838
## 2layhid4.to.3layhid8       -0.7090981377
## 2layhid5.to.3layhid8        2.0641816291
## 2layhid6.to.3layhid8        0.0521588218
## 2layhid7.to.3layhid8       -1.8200695343
## 2layhid8.to.3layhid8        2.2344182896
## 2layhid9.to.3layhid8        0.3007148270
## 2layhid10.to.3layhid8      -0.2107329397
## 2layhid11.to.3layhid8       2.3259609027
## 2layhid12.to.3layhid8       0.5015967093
## 2layhid13.to.3layhid8       0.1640478001
## 2layhid14.to.3layhid8       0.0289028202
## 2layhid15.to.3layhid8       2.0181824522
## Intercept.to.Basal-like    -1.0273462663
## 3layhid1.to.Basal-like      0.3567446669
## 3layhid2.to.Basal-like      0.1180223798
## 3layhid3.to.Basal-like     -1.8104784821
## 3layhid4.to.Basal-like     -4.0901951408
## 3layhid5.to.Basal-like     -1.5337906339
## 3layhid6.to.Basal-like      3.4030528340
## 3layhid7.to.Basal-like     -4.2622797302
## 3layhid8.to.Basal-like      1.7880475889
## Intercept.to.HER2-enriched  1.2917069887
## 3layhid1.to.HER2-enriched   0.6286408345
## 3layhid2.to.HER2-enriched   1.8483932550
## 3layhid3.to.HER2-enriched  -3.7021307748
## 3layhid4.to.HER2-enriched  -2.1093648736
## 3layhid5.to.HER2-enriched  -0.3616730271
## 3layhid6.to.HER2-enriched  -4.0336538189
## 3layhid7.to.HER2-enriched   1.4240684988
## 3layhid8.to.HER2-enriched  -4.1809403207
## Intercept.to.Luminal A     -0.3122960608
## 3layhid1.to.Luminal A      -2.9942635798
## 3layhid2.to.Luminal A      -1.7222248901
## 3layhid3.to.Luminal A       2.3290814401
## 3layhid4.to.Luminal A       3.0144641149
## 3layhid5.to.Luminal A      -2.5885986029
## 3layhid6.to.Luminal A       1.7972791038
## 3layhid7.to.Luminal A      -0.0421386180
## 3layhid8.to.Luminal A      -2.4718873405
## Intercept.to.Luminal B     -1.6173731147
## 3layhid1.to.Luminal B      -1.4130036005
## 3layhid2.to.Luminal B      -1.5131186303
## 3layhid3.to.Luminal B       0.7254037102
## 3layhid4.to.Luminal B      -2.5464566437
## 3layhid5.to.Luminal B       1.9222784362
## 3layhid6.to.Luminal B      -2.8766167110
## 3layhid7.to.Luminal B       1.3808890494
## 3layhid8.to.Luminal B       3.0433638926
neural.network.predicts_pam50 <- compute(neural.network.mod_pam50, test_data_pam50) #prediction
neural.network.res_pam50 = neural.network.predicts_pam50$net.result #results of prediction
print(neural.network.res_pam50)
##            [,1]         [,2]         [,3]         [,4]
## 3  0.9834284719 1.589789e-02 0.0030887772 0.0150598506
## 5  0.0098193804 8.589919e-02 0.4169372880 0.0004632518
## 16 0.2764088092 4.827259e-02 0.0009503088 0.2303314320
## 18 0.9887181733 1.218936e-02 0.0033357595 0.0127706408
## 19 0.9613744480 2.828674e-02 0.0125129510 0.0032593175
## 22 0.0027142116 1.952306e-01 0.0133587831 0.5728041002
## 29 0.0139484891 9.641368e-01 0.0179730849 0.0110304889
## 30 0.0019510940 1.347617e-02 0.0021737468 0.9747058766
## 36 0.0087584136 3.837981e-05 0.7867109432 0.0810311912
## 37 0.0004563222 2.588398e-03 0.9933529397 0.0042465007
## 42 0.0008912371 4.461894e-04 0.9890232756 0.0094703218
## 43 0.0027132062 6.430272e-05 0.8900424205 0.1521941542
## 48 0.0007141179 8.014605e-04 0.9932516961 0.0060452292
## 52 0.3063584568 5.718982e-01 0.0025476929 0.0494263286
## 59 0.0016574191 1.389918e-02 0.0041218125 0.9733241113
## 61 0.0015536678 1.384717e-04 0.9763511653 0.0281076367
## 69 0.0002166914 4.555793e-02 0.6341925696 0.5289693652
## 70 0.0012881583 7.019149e-03 0.0070932498 0.9788494869
## 73 0.0005593836 9.477181e-04 0.9960679323 0.0087400326
## 74 0.0017497416 5.602455e-03 0.0095940763 0.9815705593
## 79 0.0027627503 1.395436e-02 0.0022271674 0.9747154299
neural.network.res_pam50=data.frame("neural.network.res_pam50"=ifelse(max.col(neural.network.res_pam50[ ,1:4])==1, "Basal-like",
                                                          ifelse(max.col(neural.network.res_pam50[ ,1:4])==2, "HER2-enriched",
                                                                 ifelse(max.col(neural.network.res_pam50[ ,1:4])==3, "Luminal A", "Luminal B"))))
confusionMatrix(as.factor(test_data_pam50$PAM50.mRNA), as.factor(neural.network.res_pam50$neural.network.res_pam50))
## Confusion Matrix and Statistics
## 
##                Reference
## Prediction      Basal-like HER2-enriched Luminal A Luminal B
##   Basal-like             4             0         1         0
##   HER2-enriched          0             1         0         2
##   Luminal A              0             1         5         0
##   Luminal B              0             0         3         4
## 
## Overall Statistics
##                                           
##                Accuracy : 0.6667          
##                  95% CI : (0.4303, 0.8541)
##     No Information Rate : 0.4286          
##     P-Value [Acc > NIR] : 0.02405         
##                                           
##                   Kappa : 0.5392          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: Basal-like Class: HER2-enriched Class: Luminal A
## Sensitivity                     1.0000              0.50000           0.5556
## Specificity                     0.9412              0.89474           0.9167
## Pos Pred Value                  0.8000              0.33333           0.8333
## Neg Pred Value                  1.0000              0.94444           0.7333
## Prevalence                      0.1905              0.09524           0.4286
## Detection Rate                  0.1905              0.04762           0.2381
## Detection Prevalence            0.2381              0.14286           0.2857
## Balanced Accuracy               0.9706              0.69737           0.7361
##                      Class: Luminal B
## Sensitivity                    0.6667
## Specificity                    0.8000
## Pos Pred Value                 0.5714
## Neg Pred Value                 0.8571
## Prevalence                     0.2857
## Detection Rate                 0.1905
## Detection Prevalence           0.3333
## Balanced Accuracy              0.7333